Table of Contents Table of Contents...1 Chapter 1 - General Computer, Hardware, and Software Installation Information...3

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3 Table of Contents Table of Contents...1 Chapter 1 - General Computer, Hardware, and Software Installation Information...3 General Computer Environment...3 Installing the Activity Monitor Software...3 Using the Video Tracking Interface System with Activity Monitor...3 Backing Up Your Software...4 Installing the DIG-729 Control Card...4 Connecting the Activity Chambers...5 Modifying I/R Array Height...6 Chapter 2 - Getting Started...7 General Software Information...7 Introduction to Open-Field Activity Monitoring...8 Chapter 3 - Menu Options and Descriptions...10 Selecting Items from the Menus...10 File Pull Down Menu Options...10 Configuration...10 Preferences Chamber Models when using the video tracking system Experiment Configuration File Data Analysis...18 Experiment Maintenance...18 Import Data...19 Export Data...19 ENV-520 Test...21 Print...23 Session Data Data Windows Graph Windows Exit...23 View...24 Line Trace...24 Box Plot...24 Dot...24 View Summary File...24 View Analysis File...24 View Export File...25 Run...25 Open Experiment...25 Close Experiment...27 Start...27 Cancel...27 Pause...28 Resume...28 Window...28 Tile...28 Maximize...28 Restore...28 Help...28 Index...28 Using Help

4 About Activity...28 Chapter 4 - Data Analysis Menu Options...29 Data Analysis Setup...29 General Analysis Information...30 Zone Analysis...31 Rotational Behavior Calculations...34 Using the Rotational Analysis Utility...37 Save/Load Protocol...37 Chapter 5 - Inserts for Open-Field Activity...39 Dark Box Insert (Light/Dark Test)...39 Two Chamber Place Preference...40 Hole Board Task Floor...40 Chapter 6 - Setting up an Ambulatory Experiment...41 Chapter 7 - Setting up a Hole Board Experiment...49 Appendix I - File Naming and File Types...55 File Naming...55 File Types...55 Appendix II - Available Data...57 Summary Data...57 Analyzed Data...60 Hole Board Task Data...66 Exported Raw Data Files...69 Annotated...69 Stripped...70 Appendix III - Importing information from the ANALYSIS.MDB database into Excel...71 Appendix IV - Using Box Size, Resting Delay, Include Resting Delay, and Ambulatory Trigger...82 Defining Distance Traveled...82 Differentiating Between Large/Quick and Small/Slow Movements...83 Appendix V - Multiple Users...85 Appendix VI - ENV-520 Jumper Positions for Nodes 1-16 (Chambers 1-8)...87 Appendix VII - Hole Board Protocols...88 Non-Habituation Protocol...88 Habituation Protocol...88 Appendix VIII - Start on Remote Start Command

5 Chapter 1 - General Computer, Hardware, and Software Installation Information General Computer Environment The minimum recommended system is as follows: A 200 MHz or faster computer with at least one free ISA or PCI slot, or one USB port. Windows 98, 2000, or XP 64 MB of RAM (128MB of RAM if running Windows 2000 or XP) 200+ Megabytes of free disk space CD-Rom drive Mouse Installing the Activity Monitor Software Activity Monitor can be used with either the DIG-729 photo-beam system or the Video Tracking Interface system. If using the DIG-729 system; Open My Computer, open the CD drive Activity Monitor, and follow the instructions for installing the DIG-729 driver. After the DIG-729 driver has been installed, open the CD drive Activity again and click on the link to install Activity Monitor. Using the Video Tracking Interface System with Activity Monitor If Activity Monitor will be running on the same computer as the Video Tracking Interface, the minimum system requirements include: A 1.6 GHz or faster computer for one camera for two cameras, 2.9 GHz; for three cameras, 4.2 GHz; for four cameras 5.6 GHz. Windows 2000 or XP 256 MB of RAM At least one free PCI slot If Activity Monitor will be running on a different computer then the Video Tracking Interface, then a network card must be installed and the Activity Monitor computer must be able to see the Video Tracking Interface computer over the Windows network. To install Activity Monitor, open My Computer, open the CD drive Video Tracking, and click on the link to install Activity Monitor. Now please skip to Chapter 2 Getting Started. 3

6 Backing Up Your Software We strongly encourage you to make a backup copy of any data files created by Activity Monitor (especially the file DEFAULT.ZIP) in case of a disk failure. Installing the DIG-729 Control Card Note: Always turn off the power before working on the computer or chambers. Neglecting this precaution may cause serious damage. If you have a DIG-729 PCI card, install the DIG-729 card in any available PCI slot, following the instructions provided with the computer for installing a PCI card. If you have a DIG-729 ISA card, install the DIG-729 card in any available ISA slot, following the instructions provided with the computer for installing an ISA card. The Interrupt Request (IRQ) number may be changed from the factory default of 5 by moving the jumper on J4 to 3, 4, or 7 (Figure 1.1). This should not be done unless there is a conflict with another device in your system. The base address also should not be changed unless there is a conflict. Figure DIG-729 ISA Switch Locations and Jumper Settings Figure Activity Chamber Setup 4

7 Figure Activity Chamber Setup with Hole Board Insert Hole Board Transmitter 1 and Hole Board Transmitter 2 get connected to the Transmitter 3 port on the ENV-520 Controller. Hole Board Receiver 1 and Hole Board Receiver 2 get connected to the Receiver 3 port. Transmitter 1 gets connected to the Transmitter 1 port. Transmitter 2 gets connected to the Transmitter 2 port. Receiver 1 gets connected to the Receiver 1 port. Receiver 2 gets connected to the Receiver 2 port. Connecting the Activity Chambers Connect the DIG-729 computer card to the ENV-520 Controller on Chamber #1 with the 15 pin SG-219C control cable. Note: The chambers are labeled on the ENV-520. This number is factory set with jumpers inside the ENV-520 and should not be modified unless necessary (Appendix VI). Additional chambers are connected via their ENV-520s controllers with SG-219C control cables, starting at Chamber #1 and proceeding in sequence, in a daisy chain fashion. For example, if you have four chambers, Chamber #1 connects to Chamber #2, Chamber #2 connects to Chamber #3, and finally Chamber #3 connects to Chamber #4. Ensure each connector is securely attached to the ENV-520 by tightening the screws on the cable. Connect the power cords from all ENV-520s to the SG-506 power supply (see ENV-520 Test Chapter 3) for a quick hardware test utility that can be run to verify proper operation of all photo beams before actually running an experiment. 5

8 MED Associates assembles equipment prior to shipment. The ribbon cables are connected from the ENV-520 to the I/R Array Strips as shown in Figures 1.2 and 1.3. The corresponding receiver strips are located directly opposite the transmitter strips. Modifying I/R Array Height The photo beams that are used to detect subject movement are located on the Infrared (I/R) Array strips. Since experimental subjects vary in terms of size, we recommend adjusting the height and position of the I/R Array strips to match the physical characteristics of your particular subjects. Also, adjusting the I/R Array strips is necessary if you intend to use experimental inserts (e.g. place preference or hole-board inserts, Chapter 5). Position the lower (X & Y-axis) I/R Array strips so that they are best aligned with the subject s vertical center. If the lower I/R Array is positioned too high, a subject may be capable of crouching below the array, and no data will be obtained for that moment in time. There may be other scenarios wherein inaccurate I/R Array placement may create erroneous data, so use care in this process. The Z-axis I/R Array (the second row of strips) is used to detect rearing and other verticalmovement behavior. The Z-axis I/R Array should be placed in the lowest possible position capable of detecting vertical activity and not detecting normal "X" & "Y" activity. Position the Z- axis I/R Array just above the subject s spine. If these strips are too high, some rearing behavior may not be detected. If the Z-axis strips are positioned too low, a slight "bouncing" by the subject may be detected as rearing. Note: We suggest conducting a pilot study using your particular subjects within the open field activity chamber to determine the best heights for all I/R arrays. 6

9 General Software Information Chapter 2 - Getting Started To meet the current demands of behavioral research, Med Associates OFA (Open Field Activity) systems offer a variety of data analysis options such as measures as rotational behaviors, zone entries, jumping, etc. (Appendix II, Available Data). Data acquired on older systems using version 3.0 or higher may be reanalyzed with our new software to obtain these new measures. The Activity Monitor is designed for use with MED Associates hardware to collect, plot, and analyze activity data. All standard data is displayed in real-time, along with a cumulative plot of the subject's activity. The data acquisition configuration files, which specify the state of the system (Resolution/Sample Rates, Ambulatory/Stereotypic Movement definitions), are stored in filename.cfg files. See Chapter 3, for Configuration File set up. In addition to providing the database to store all experiment and subject data and information, we have also provided the option to create an ASCII text and a "hard copy" printed-summary data file automatically. After each session or after each experiment (multiple subjects/sessions), the software can print the summary data automatically and save a summary data file for each subject. Accomplish this by checking the appropriate boxes in the preference settings window (Figure 3.3). Likewise, analyzed data and Raw Point data ASCII text files may also be generated aside from the database file. All ASCII text files are named according to the filenaming scheme presented in Table 3.5 and discussed in Appendix I. There are two database files created by the Activity Monitor software: EXP.MDB and ANALYSIS.MDB. These files are Access database files, but may be opened with many database programs. In order to extract precisely formatted data, they must be manipulated or sorted with a database program that can open a standard Access scheme. We have created this database capability to enable researchers to export an entire experiment s worth of analyzed data into a spreadsheet to make statistical analysis as easy as possible. 7

10 Introduction to Open-Field Activity Monitoring Open-Field Activity (OFA) monitoring is a sensitive method of measuring both gross and fine locomotor activity in small animals. In general, computerized OFA characterizes multiple end points of motor behavior, and as such, has proven to be a powerful assessment tool with many applications in behavioral pharmacology, toxicology, and genetics. For example, dopamine agonist studies can use distance traveled in centimeters as a measure of gross motor activity that is amenable to quantitative analysis. Opiate tolerance studies can examine overall distance traveled, and can also utilize time and distance in a margin of the chamber as well. Anxiety can also be characterized with an OFA system using the aforementioned measure and by examining patterns of exploration in a brightly lit arena with a dark area (i.e. place preference task, see Dark Box Insert Light/Dark Conflict Test, Chapter 5). In addition, other experimental procedures with proven construct validity, such as the hole-board task, can also be performed with the MED Associates OFA System. Add-on components and inserts make the MED Associates OFA system very versatile and an excellent value for laboratories that are both space and cost conscience. Two standard sized environments, the ENV-510, 10.75" X 10.75" X 8" H (27 X 27 X 20.3 cm) and the ENV-515, 17" X 17" X 12" H (43.2 X 43.2 X 30.5 cm) are suitable for mouse and rat protocols, respectively. The system consists of a subject containment environment (chamber), infrared (I/R) transmitters and receivers, a system power supply, an environment data source controller, appropriate connecting cables, a PC/environment interface card, and data acquisition/analysis software. Subject location is tracked using 16 evenly spaced I/R transmitters and receivers positioned around the periphery of the chamber. This I/R Array defines the X, Y, and Z coordinates used to create a map of the arena. The sensors detect the presence or absence of the I/R beam (i.e. the subject) at these corresponding coordinates. At user defined time intervals, the software has instructions to poll the environment for the presence or absence of the I/R beam at each sensor. This is the scanning rate or sampling rate of the system (Figure Resolution (ms)). If the I/R beam fails to reach the sensor, the system registers this event as a broken beam and assumes the presence of the subject. For instance, broken beams at positions X 1,2,3,4 and Y 2,3,4,5 are averaged, with the resulting microprocessor derived coordinate being X = 2.5 and Y = 3.5 or just 2.5, 3.5. The averaged beam breaks or subject "centers" are the data that the software algorithms use to derive the behavioral parameters such as distance traveled and time spent in a given zone. By scanning the environment many times a second, the OFA system can effectively track the movement of a subject very precisely. The faster the scanning rate, the greater the accuracy of the system for high-speed behavioral measures such as stereotypic behaviors (e.g. grooming), as well as for event-related, time-sorted measures. We offer the opportunity to use a range of scanning rates to accommodate personal preferences (Table Resolution). Many researchers feel that there are few advantages to faster scanning rates for long trial runs where the data of interest do not require the increased rates. After all, faster scanning rates mean larger data files and longer post-hoc data-analysis processing times. 8

11 The software included in the OFA package allows the researcher to capture data in small samples repeated at preset intervals (Figure 3.5, Table 3.2, Segmented Data Files). This virtually eliminates the need to sort through large quantities of data to extract the desired measures. Experience in this matter will help you to determine the Session Type (continuous or segmented, see Chapter 3) and the scanning rate resolution that is best for you and your applications. We are now ready to walk through the menu selections. In the next chapter, you will learn how to define the parameters of the experiment. To best become familiarized with the apparatus, we recommend running a few pilot sessions before collecting experimental data. 9

12 Chapter 3 - Menu Options and Descriptions To run the Activity Monitor, select the Activity Monitor program group and double click on the Activity Monitor icon. The main Activity Monitor screen appears with a copyright screen that disappears after a few seconds (Figure 3.1). Figure Activity Monitor Copyright Screen The main Activity window is now displayed with a menu across the top of the window, and these menu options are listed below. Selecting Items from the Menus File Pull Down Menu Options Configuration Select File Configuration to define the options pertinent to your particular experiment. Defining and saving a configuration will eliminate the need for you to enter the parameters every time you run an experiment. Listed under the Configuration option (Figure 3.2) are Preferences (Figure 3.3) and Experiment (Figure 3.4 and 3.5). The default settings are user-defined and are determined the very first time that the Activity Monitor software is run. The filename.cfg file controls how the software acquires the behavioral data. This file defines the sampling rate, session time, and other important parameters of your experiment (Figures 3.4 and 3.5). The raw data is automatically compressed in a filename.zip file. Within this ZIP file are the raw binary data files that are named according to the date on which they were created (mmddyyyya0 - Z99, i.e A0 (January 1, 2003), and are linked to the subjectappropriate data file. These filename.zip are the files used by the system for playback and analysis. The settings in the Preferences window may be changed at any time but may change the nature of summary data; therefore, we do not recommended that you modify these settings in the middle of running an experiment. Experiment configuration settings cannot be changed in the middle of an experiment. 10

13 Figure File pull down menu Figure The Preferences Screen defines computer and hardware options. Changes here will affect data acquisition as well as data analysis for both imported data files and/or system-generated files. 11

14 Figure The Experiment Configuration File Screen sets data acquisition and ambulatory data parameters. Included in the Experiment Configuration File are the settings necessary to run a Hole Board test and to choose session type. Figure Experiment Configuration File Screen with the S (Segmented) Session Type selected. 12

15 Preferences (See Figure 3.3 and Table 3.1 for details) File Configuration Preferences contains a number of selections that define the nature of the Summary Data. Carefully select the appropriate Chamber Model to reflect your current system. The preferences screen requires the following information: Item Data Directory Name: Description The directory to store the data (*.ZIP) files. If you are unsure which directory to use, use the browse button. We advise creating a subdirectory named DATA in the Activity Monitor directory, and use this subdirectory whenever storing *.ZIP files. Also, this directory will be the directory where the database files (EXP.MDB and ANALYSIS.MDB), Summary, and Zone Analysis text files will be located. Multiple users can use the OFA monitoring system and have their own separate database of experiments. See Appendix V for details. Data Reporting Mode: A = Absolute R = Relative Experimental sessions are divided into intervals called Time Bins. In Absolute mode, each time bin holds the sum of all of the data since the experiment began. In Relative mode, each time bin holds the sum of the data since the last time bin. The Data Reporting mode affects how the data look when sent to the printer, and how the data look in the Summary Data file. The Data Reporting mode is also used to determine how the data will be presented in the Analyzed Data files. Display Time in Hours Units Number of Chambers Chamber Models When checked, this option displays time as hours:minutes:seconds (000:00:00.00). If unchecked, time is displayed in minutes as minutes:seconds (0000:00.00). Determines the units of distance traveled, in centimeters or inches. The number of test chambers being used (1 8). The test chambers always start at 1 and proceed in sequence (see Chapter 1, Connecting the Activity Chambers). Provides the chamber product number: ENV-510 for X (mouse) chambers with 16 beams ENV for 17 X 17 (rat) chambers with 16 beams ENV for 17 X 17 (rat) chambers with 32 beams VID-510 for X (mouse) chambers for use with Video Tracking Interface VID-515 for 17 X 17 (rat) chambers for use with Video Tracking Interface VID-410 for 7 X 9.5 (mouse) home cages to be used with Video Tracking Interface VID-415 for 8 X 17 (rat) home cages to be used with Video Tracking Interface Carefully select the correct chamber so that distance traveled data is calculated correctly. Print Off (does not print the data file) Session End (prints the data file after each experimental session) Experiment End (prints the data file when Run Close Experiment is selected) Use this feature to create a hard copy of each experimental session. Justify Select Right or Left to justify the data accordingly. 13

16 Item Include Resting Delay Generate Summary File Automatic File Naming Start on Animal Entry Start on Remote Start Use Video Tracker Description As detailed in Appendix IV, the "Box" serves to filter movement data for a precise distancetraveled measure. Selecting Include Resting Delay removes the resting delay filter from the distance-traveled measure, meaning that the time the subject spends resting will be included in distance traveled. Therefore, Include Resting Delay should not be selected unless you are attempting to duplicate data that was generated on a system that does not have this "filtering" capability. This option creates an ASCII text summary file that will be automatically saved in your data directory. The file will also have the extension SUMMARY. This option allows the user to store the summary data, which may also be printed, for backup. Creates data filenames according to the file-naming scheme presented in Table 3.5 and Appendix I. If the Automatic File Naming option is selected, then the file name is generated automatically from the values entered into the Subject, Experiment, and Group fields on the Run Experiment screen (Figure 3.15). If this check box is not selected, the User must manually enter a file name. Enables the system to begin a session as soon as the subject is placed into the chamber. This feature cannot be used with a Video Tracking Interface. Enables the system to begin a session as soon as the Remote Start Event for that chamber has been set, thus allowing 3 rd -party programs (like MED-PC IV) to remotely start the Activity chamber. If both Start on Animal Entry and Start on Remote Start are checked, the chamber will not start until it has received a Remote Start Event and the animal is present in the chamber. See Appendix VIII for more information on the Remote Start command. This feature must be enabled to use video-tracking equipment in conjunction with the OFA system. Select Computer Source When using a Video Tracking Interface (VTI), this option selects the computer used by the VTI to capture data. In Windows 98, this information must be manually entered. For example, if the VTI software is running on the computer video, then enter the text \\video into the available display. In Windows 2000 or XP, click on the Select Computer Source button to browse for the appropriate computer. If Activity Monitor is running on the same computer as VTI then select My Network Places, as shown in Figure 3.3. Table Preference Configuration Options Chamber Models when using the video tracking system Activity Monitor can acquire data for eight different test subjects simultaneously, as indicated by the drop down menus numbered 1 8 in the Chamber Models field of the Activity Monitor Preferences screen shown in Figure 3.3. Video Tracking Interface (VTI) can acquire data from four cameras, depending upon the capabilities of the computer, and each camera can track either one, two or four animals depending upon the type of chamber/cage platform you will be using (i.e. VID-515, single rat activity chamber; VID-510, dual mouse activity chambers; VID- 415, dual rat home cages; VID-410, quad mouse home cages). 14

17 When Activity Monitor is using VTI to acquire data, the chamber model needs to be selected for each test subject (1 8, as appropriate). The chamber model is dictated by the number of cameras used by the VTI and also by the particular chamber/cage platforms being used. Using two cameras to capture video data: VID-515 tracks one animal per camera, so chambers 1 and 2 should be set to VID-515. VID-510 & VID-415 capture data from two animals per camera, so set chambers 1 through 4. VID-410 acquires data from four animals per camera, so set chambers 1 through 8. Experiment Configuration File (See Figures 3.4 & 3.5 and Table 3.2 for details) File Configuration Experiment opens up the Experiment Configuration File. The Experiment Configuration File contains a number of entries that determine the nature of acquired Summary Data, and these settings may be modified in Data Analysis to examine the parameters in greater detail. Included in the Experiment Configuration File is the Hole Board Task definition (see Chapter 7, Setting Up A Hole Board Experiment). Save your newly defined settings as DEFAULT.CFG using the Save As or OK buttons. You are now ready to run your first experiment using these settings. We recommend that the file names for configuration files reflect the protocol that you wish to run. For example, changes in Box Size, Ambulatory Trigger, and Resting Delay (Table 3.2) for use in amphetamine studies could have a filename that reflects its usage, like Amphetamine_Box_Size.CFG. DEFAULT.CFG should be used for your first practice experiment and kept on the computer in the Activity Monitor directory. Note that once an experiment is started with a specific configuration, it cannot be changed mid-stream. The reason for this is to maintain parameter continuity throughout an experiment. The Experiment Configuration File requires the following information: 15

18 Item Resolution (ms) min - 25 max 250 Description Resolution is the rate that data is acquired from the test chambers, and is user-definable to enable variable data acquisition rates. Select a large number (>100 ms) to minimize file size and data-analysis computing times if you are using an older PC system. Since hard disk memory capacity is not a limiting factor on most new systems, we recommend entering 50 ms or less to maximize data resolution. Resolution is automatically set to 33 1/3 ms when using the Video Tracking Interface system. Box Size (beams) min - 1 max 8 Box Size serves three primary functions: 1) Box Size delineates the maximum area that a subject may move within (after the Resting Delay criteria has been met, see below), and movements within this box are used to calculate Stereotypic Count. Stereotypic Count refers to any partial-body movements that occur within a defined space, such as grooming, head-weaving or scratching movements. If Stereotypic Count is the primary measure, Box Size should be set to the maximum space within which partial-body movements can occur. 2) Box Size filters movement data so that distance-traveled measures do not include "bouncing" or "flickering" artifacts. 3) Box Size, Ambulatory Trigger (see below), and Resting Delay settings combine to create a threshold whereby a subject must move a certain distance (Box Size) in a maximum amount of time (Resting Delay) to maintain its ambulatory status. Define these parameters to best capture large (whole-body or ambulatory) and small (partial-body or stereotypic) movements. See Appendix IV for details. Standardized settings are not available, and are dependent upon the application being used (ataxic vs. non-ataxic subjects) and the strain of rodent being studied. Box Size can also be changed in Data Analysis. Resting Delay (ms) min - 50 max Resting Delay defines the amount of time that needs to pass before a current Ambulatory Episode is terminated. The Ambulatory Episode refers to a time period during which whole-body movements are recorded. In Data Analysis, the number of Ambulatory Episodes reflects the number of times the subject has started moving after the Resting Delay has expired (see Appendix IV). Resting Delay can also be changed in Data Analysis. Ambulatory Trigger When a subject moves outside of the defined Box Size (see above), Ambulatory Trigger refers to the number of I/R photo-beam breaks necessary to initiate an Ambulatory Episode after the Resting Delay has expired. Session Type (C, S) Select "C" for a Continuous session. Select "S" for a Segmented session. If a Segmented session is chosen, the Experiment Configuration File display changes, as shown in Figure 3.5. Session Time (min) Session time defines the duration of the experimental session, in minutes. Block Interval (sec.) Block Interval determines the duration of time that the session data are to be divided for Data Analysis. Therefore, Block Interval defines the duration of the time bin (see Data Reporting Mode in Preferences, above). If Session Time = 60 min, and Block Interval = 30 sec, then the number of time bins = 120. Block Interval may also be changed in Data Analysis. 16

19 Item Compressed File Hole Board Floor Installed Hole Board Strips Installed Description Name of the *.ZIP file to store the raw data. If an extension is given, it will be ignored (see Appendix I). Refer to Appendix V for multiple users. This option must be checked if the Hole Board Insert (Appendix VII) is being used. Please note that the Video Tracking Interface cannot be run in conjunction with the Hole Board Insert. This option must be checked if the Hole Board I/R (4 x 4) arrays are being used to run the Hole Board Task test and the X and Y photo beams are being used to monitor general activity (see Appendix VII). Define Task Floor Click to view the task-definition screen (Figure 7.4). Total Session Time (min) Sample Time (min) Sample Interval (min) The total length of time that the experiment will take. This is the same as Session Time; however, we have differentiated this parameter for simultaneous use in Segmentedsampling configurations (see Session Type, above). The duration of time during a Sample Interval (below) during which data will be acquired. This is the total of the Sample Time and the Time-Out Interval for one session. For example, if the Sample Time is 3 min and the Time-Out Interval is 2 min, then the total Sample Interval will be 5 min. Number of Samples The program automatically calculates the number of samples that will be taken during Total Session Time. Therefore, the Number of Samples is dependent upon Sample Time, Sample Interval, and Total Session Time. Time-Out Interval (min) Load Save Save As... OK Cancel The amount of time that data will not be taken during each Segment. The program will automatically calculate the value from the Sample Time and Sample Interval. This option allows you to select the Experiment Configuration File that will be used by the program to determine the data properties. Saves the present configuration information to the already named filename.cfg. For new configurations, use the Save As option. Brings up a Save As window so you may specify a filename. When setting up the software for the first time, use the DEFAULT.CFG file name automatically specified in the Save As window. This default configuration will then be readily available whenever beginning a new experiment. After loading, changing existing, or creating new *.CFG files, this option allows you to exit the Experiment Configuration File window. Exits the configuration screen without saving the information. Table Experiment Configuration Options 17

20 Data Analysis The File Data Analysis option brings up a listing of data files for analysis or re-analysis. The data files are in the database EXP.MDB and are separated by Experiment ID. You can find a specific data set/session by clicking on the corresponding experiment (top list Figure 3.6) and scrolling through the individual subject data sets (bottom list Figure 3.6) until you find the desired subject/session data. Figure 3.6 shows the screen displayed when the Data Analysis menu option is selected. Chapter 4 - Data Analysis, has the necessary detailed information for you to analyze your data. To select the data to be analyzed, simply click on the subject/file name on the lower half of the screen display to activate that file. Select more than one file to analyze by using the Shift key. You may resize column widths using your mouse and clicking in the header row. Figure Data Analysis Window for selecting data to be analyzed Experiment Maintenance File Experiment Maintenance allows you to view, print, and delete the information in the database (Figure 3.7). If you cancel a session in the middle, you may decide not to keep the data. You can find a specific data set/session by clicking on the corresponding experiment (top window Figure 3.7) and scrolling through the individual subject data sets (bottom window Figure 3.7) until you find the undesirable subject/session data. To delete the data, left-mouse click on the corresponding line and then click the delete button. The Print button can be used to reprint the Summary data file that was created during the experimental session. You can choose to have the data printed in either Relative or Absolute mode (see Preferences, Data Reporting Mode). If the data has been imported from a *.Zip file, then it is not possible to reprint the Summary data file. 18

21 Figure Experiment Maintenance Window is used to print summary data or delete unwanted session or experiment data files Import Data The File Import Data option allows the user to import data acquired with this version and earlier versions of the Activity Monitor software, store the data in the database, and analyze this data with the up-to-date measures. You may import multiple *.ZIP files by using the Shift or Ctrl keys when you select the files. Like data files that are created when you run an experiment, data files that are imported are reformatted and stored in the raw data *.ZIP file (Table 3.2). Export Data The File Export Data option allows you to select a file and save the data as an ASCII text file with a filename generated according to the Data Filename scheme presented in Table 3.3, with an EXPORT extension. This utility is available for those researchers who may wish to analyze their data by writing a program in Visual Basic or some other language. Once a pattern is identified, the only way to extract very complex behaviors may be to do your own programming. We design software with the most commonly used measures, and of course, some novel ones too. However, some researchers may be interested in a specific behavior for which we have not created a standardized measure. Therefore, saving files in ASCII format allows for the analysis of undefined behaviors. After selecting a data file, the Save Raw Data screen (Figure 3.8) appears. Click on the file that you wish to export. Another screen will appear (Figure 3.9) and request the following information: Item Annotated File / Stripped File Description Select the type of file output you prefer. The annotated file includes the experiment header information. The stripped file only includes the point-data information. When importing information into a spreadsheet, we advise including the annotated file for the first data file and stripped files for each subsequent file. 19

22 Item Time: Save As Cancel Description Select the time period, in minutes, you wish to include in this file. You may specify any part of a session or the entire session. Use this method to save time by exporting specific, time-sorted, sections of the data. Clicking on this button will bring up a Save As file screen so you may enter the filename for the point data. Exits the Save Raw Data screen without saving the data. Table Saving Point Data as an ASCII File Figure Export Raw Data Screen to select files for conversion to ASCII Figure Save Raw Data type definition screen 20

23 ENV-520 Test... The ENV-520 Test provides a graphical interface for testing the ENV-520 controller, photo beam strips, and the interrupt on the DIG-729 card for each chamber (Figure 3.10) and for all chambers simultaneously (Figure 3.11). Also, you can use the ENV-520 Test for the Video Tracking Interface (VTI) system. The ENV-520 Test should be conducted before every session. First, run the multi-chamber test by checking the Display Raw Values check box. Make sure that there are no subjects in the chambers. Click Start. If the X, Y, or Z values are any number other than zero, check for obstructed photo beams. The number of beam breaks should be zero. If there are multiple beam breaks on the X, Y, or Z-axis when no subjects are in the chamber please contact MED Associates. If there are many chambers (nodes) with values other than zero, contact MED Associates. With the ENV-520 test running, run your hand through the arena of the activity chamber and monitor the X, Y, and Z coordinates on the ENV-520 test display. The X, Y, and Z coordinates should indicate the position of your hand in the arena. If certain X, Y, and Z coordinates fail to register your hand movements, double check to make sure that the right chamber model (e.g. ENV for 17 X 17 with 16 beams) has been selected. ENV-520 Test Menu Options: Item Description Select Chamber Select the chamber number you wish to test. Only 1 chamber can be tested at a time. Display Raw Values This allows you to see the bit values for all chambers simultaneously. Tick Count Time increments Start Click this button to start the test. Photo beams that are blocked or not functioning, displays as a red dot. Functioning photo beams display with a gray dot. Stop Clicking on this button stops the interrupt and stops displaying data. Exit Exits the ENV-520 Test screen. Using the ENV-520 test for VTI Table ENV-520 hardware test utility First, make sure that the preferences menu is set to Use Video Tracking. Then start capturing data on the VTI system and then run the ENV-520 Test to ensure that the equipment is in proper working order and to identify where hardware problems may be occurring. Should you have problems with your system, contact MED Associates for help troubleshooting. 21

24 Figure ENV-520 Test Screen to isolate blocked or non-functioning photo-beams. Figure ENV-520 Test Screen for all chambers. 22

25 The Node number represents the chamber number. If the number displayed in the X, Y or Z columns is greater than 0 for an empty chamber, then there is a problem with that chamber. The binary number displayed represents the I/R photo beam(s). Print Print is only available after an experiment finishes running or after data has just been analyzed. Different menu options are available depending on whether an experiment finished or data was played back. Figure Print options are available after running an experiment or analyzing data. Session Data Session Data, Data Windows, and Graph Windows options are only available after the completion of an experiment. The Session Data option prints the selected chambers' summary data files to the default printer. This same option can be activated to automatically print by selecting the Print on Session End or Experiment End button on the File Configuration Preferences screen (Figure 3.3, page 11). Data Windows The Data Windows menu option prints the selected chambers' data windows to the Windows default printer. Graph Windows This menu option prints all the chambers' graph windows to the Windows default printer. Exit Exits the Activity Monitor program. If an experiment is running, the data saves and prints in the same fashion as canceling an experiment. 23

26 View Use the View pull-down menu options modify the real-time display of the subjects' activity. These options also change how the data are displayed for the Data Analysis utility should you choose to activate the Display Grid option during Data Analysis (see Chapter 4). Figure View pull down menu options determine grid/subject viewing types Line Trace The Line Trace option is the default and plots a dot as the midpoint of the subject (the average of X-Y beam interrupts) and draws a line to show all movement. Box Plot The Box Plot option shows the stereotypic box around the midpoint of the subject (see Box Size under Experiment Configuration, pg. 15). The subject can be seen moving within the box during stereotypic movements. When the subject becomes ambulatory, the box adjusts to represent the new midpoint of the subject. Dot Select the Dot option to plot the midpoint of the subject only. View Summary File The View Summary File option will open and let you view the contents of your summary data files (files that have the SUMMARY extension). View Analysis File The View Analysis File option will open and let you view the contents of your data analysis files (files that have the ZONE extension). 24

27 View Export File The View Export File option will open and let you view the contents of your exported data files (files that have the EXPORT extension). Run The Run pull-down menu options allow you to execute, pause and close the experiment. Figure Run pull down menu options. Open Experiment Select Run Open Experiment to display the Run Experiment window that is the heart of this program. The Run Experiment window (Figure 3.15) is the interface between the execution of experiment and data acquisition and storage. Since the Open Experiment menu option is actually the first step taken toward running the experiment, the majority of the associated information can be found in Chapter 6 - Setting up an Ambulatory Experiment. Figure Run Experiment Screen with experiment specific and subject specific information, linked in a database. 25

28 Text boxes for Subject ID, Experiment ID, and Group ID include pull-down menus. The automatic selection of the Start Box (check box) begins the experiment as soon as OK is clicked. If the Start on Animal Entry check box (in the Preferences screen, Figure 3.3, page 11) is activated, the session will start as soon as the subject is placed into the chamber. The Run Experiment window requires the following information: Item Current configuration: Experiment ID: Description The current system configuration filename is displayed at the top of the experiment setup screen when creating a new experiment. The Browse button located at the top right of Figure 3.15 allows you to find a configuration file that is appropriate for the type of experiment you wish to run (Figures 3.4, 3.5 and Table 3.2). The Experiment ID may be up to 25 characters and is used for both the Data Filename (below and Appendix I) and as a link throughout the database to sort data. This field is used to automatically generate the Data Filename (below). There is a pull-down menu associated with the Experiment ID that will contain subject information and experiment configuration parameters once an experiment is executed and saved. Experiment Title: Experiment Comment: The Experiment Title may be up to 25 characters. This is a descriptor field for the Experiment ID. When you open the Data Analysis or Experiment Maintenance windows, the Experiment Title is visible. This description of the experiment is present to allow you to visualize which data sets you may select for analysis, re-analysis, deletion, etc. This field is maintained for database purposes and allows you to add additional information pertaining to a given experiment. The above 4 data entries are experiment-specific in nature. The information entered here is included in the database for all subjects run under the specified Experiment ID and Title. These data will also have been collected using the Configuration file (Figures 3.4, 3.5 and Table 3.2) and will include the Experiment Comment. Box # 1-8 Index Card Tab Session Comment: Subject ID: Session: Group ID: Activates the data entry screen specific to a particular chamber. All comments entered in this screen are added to each subject s session data file. This field is used as a subject identifier, with 25 available characters and automatically generates the Data Filename (below). The Session field is automatically generated by the database program. The first time that an experiment is started and a subject s information is entered, the session # will be 1. Each subsequent entry of that Subject s ID automatically enters the corresponding Group ID and generates the next Session # in sequence. The database links Experiment ID information to Subject ID information, tracks the number of sessions and sorts the information and data accordingly. If a session is deleted, the database skips that session number. If all session files are deleted for a given subject and the subject is re-entered, the sessions will again start at 1. This field is used as an identifier, with 25 available characters, and is linked to the Subject ID the first time that a subject is run in an experiment. This field is used to automatically generate the Data Filename (below). 26

29 Item Data Filename: Start Box Copy Data to All Chambers Clear Data OK Cancel Description All Data Filenames are generated using the Subject ID, the Group ID, and Experiment ID. See Appendix I - File Naming Schemes, File Types, and Formats for details. If automatic file naming is turned off you may enter your own filename. This check box is used to tell the software to start the chamber when OK is clicked. If the Start on Animal Entry check box is activated in the Preferences screen and saved in the current *.CFG file, then the session begins as soon as the subject is placed into the chamber and the first photo beams are broken. Copies the information in the current screen to all the other chambers. All data is copied except the Subject ID. This feature is very useful to speed up data entry. Clears all the data fields. If the Start Box check box is activated, selecting OK closes the Chamber ID screen and starts the experiment. Closes the Run Experiment screen without running the experiment and deletes all chamber/subject-specific information entered. The above five data fields are subject specific in nature and are added to a given subjects data file accordingly. This information is only linked to chamber-specific information for a given session. The above two fields are chamber-specific in nature and reflect the state of a given chamber during a given session. Table Experiment database and run screen continued Close Experiment Select Run Close Experiment to abort a running experiment or close the run-screen when all subjects have finished. If you have chosen to print data at the end of an experiment (Figure 3.3), the summary data file will print at this time. All the data that has been collected up until the time that the experiment was canceled, if still active, saves using the file names specified during Experiment Setup (Table 3.5 and Appendix I). If you need to delete aborted experiment data files, it is best to do so immediately via the Experiment Maintenance window (Figure 3.7). Start The Run Start option displays the Run Experiment screen (Figure 3.15), where the subjectspecific and chamber-specific information (Table 3.5) is entered. Clicking OK starts the session. Cancel The Run Cancel option stops the session and closes the experiment for those chambers which have been selected. All captured data up until the cancel was initiated is saved to the corresponding subjects' file. You may delete session data using the Experiment Maintenance utility (Figure 3.7). 27

30 Pause The Run Pause option allows the operator to pause the data acquisition for a selected chamber and resume (below) when applicable. Resume The Run Resume option resumes paused data acquisition (above). Window Tile Arranges the windows in a tile fashion. Maximize Maximizes the active chamber s display window. Restore Restores the chamber-display windows to tiled. Help Index Opens the Activity Monitor Help file and brings up the index. Using Help Opens Window's How to Use Help file. About Activity Displays the Activity Monitor copyright and version screen. 28

31 Chapter 4 - Data Analysis Menu Options Data Analysis Setup Figure Data Analysis Database Window After running an experiment, select File Data Analysis to view a listing of experiment and subject/session data files (Figure 4.1). Once you have selected the appropriate experiment and subject, click on the OK button and the Data Analysis screen appears (Figure 4.2). This screen is divided into three categories, General, Zone Calculations, and Rotational Calculations. This screen displays selected parameters that are set in the corresponding Select Definition windows of the program (Figures ). Figure Data Analysis Screen 29

32 There are five check boxes that control the following: Item Description Rotational Analysis Activates the select definition bar to define the rotational behavioral analysis. These parameters are defined in the corresponding Select Definitions display window (Figures ). Activation of the check box increases your analysis time considerably. Zone Analysis Display Grid Write Summary File Create Database Entries Activates the select definition bar to define the zone analysis. These parameters are defined in the corresponding Select Definitions display window (Figures ). View subject movement graphics and the associated measures while the data are being analyzed. This is nice to see when you first run the program; however, when analyzing multiple data sets (perhaps 100s) this feature slows down the analysis time considerably. This option also allows you to print movement plot graphics at the end of the analysis. Automatically generate an ASCII text file of the analysis data. These summary analysis data files are named according to the file naming structure (Table 3.5 and Appendix I). Every time that a subject is run and the data is analyzed or re-analyzed, the associated data measures are appended to the file. These data are always in the common subject data file. The same analysis information is also present in the ANALYSIS.MDB database file. Create ANALYSIS.MDB database entries of the analyzed measures. Both ASCII text and database files are generated if both Write Summary File and Create Database Entries check boxes are activated. Table Data Analysis file, display and analysis selections. General Analysis Information Figure General Analysis - Continuous Experiments Figure General Analysis - Segmented Experiments 30

33 The first Select Definition category is for General Analysis. These parameters were established in the Experiment Configuration setup, but may be modified for data analysis. The following parameters may be changed in the General Analysis section: Item Start Time default 0 (min) End Time default - end time Sample Number Data Block Interval (seconds) Data Blocks Numeric Description Defining this option starts data analysis at a time point other than the beginning of the session (zero). define this option Select the minute that you want to start the data from. Like End Time, listed below, this feature is useful primarily only after data has already been analyzed and specific time bins need to be further defined. Select the minute at which you want the data analysis to stop. The default is the end of the session. This feature is useful primarily after data has already been analyzed and specific time bins need to be further defined and analyzed using, usually, smaller time blocks. If Segmented Experiment was selected, then the Sample Number option will appear instead of the Start Time and End Time options. The Sample Number option allows you to select which time segment you wish to have analyzed. Data may be analyzed as a series of time blocks. This feature is useful for examining instantaneous values (1 sec) or larger to for time-sequenced or eventrelated analysis. The Data Block Interval is independent from the Experiment Configuration Block Interval (Figures 3.4 and 3.5), and this value may be changed for each data file re-analysis. The number of Data Blocks established when the analysis time (entire session or a portion there of as defined by the Start and End Time listed above) is divided up by the Data Block Interval. Box Size (beams) See Experiment Configuration File. min - 2 max 8 Resting Delay (ms) See Experiment Configuration File. min - 50 max Ambulatory Trigger See Experiment Configuration File and Appendix IV. Table 4.2 General Data Analysis Zone Analysis The Zone Setup screen allows you to define the X and Y coordinates of the zones you wish to differentiate and analyze. All of the behavioral measures will then be determined for each zone, as well as totals for all zones. Up to 4 zones plus 1 residual zone may be created or selected (Figure 4.5). A number of preset zone options have been provided. They include Horizontal, Vertical, Quadrant, Corner, and a number of user-defined spaces for custom zones (Figure 4.6). The user-defined zones must be rectangular in shape and cannot overlap one another. Any part of the activity area that is not defined within a zone is counted as the residual area (Figures 4.5 and 4.7). 31

34 Figure Zone Setup Screen showing Pre-Defined menu options and Residual Area Figure Save customized zone settings 32

35 Figure Use of the residual area configuration The Zone Setup screen requires the following information: Item Number of Zones Pre-Defined Start X Start Y End X End Y Display User-Defined Settings Save Save As OK Cancel Description This pull down window allows you to select from 1 4 zones. There are actually five possible zones of analysis, the number selected with this item and a residual zone. A number of pre-defined zones present with each number of zone settings (Figure 4.5). You may use these pre-defined settings or configure your own. The starting X-coordinate for the zone you are defining. The starting Y-coordinate for the zone you are defining. The ending X-coordinate for the zone you are defining. The ending Y-coordinate for the zone you are defining. Displays the zones you have defined in the Zone Display on the bottom of the screen. Using the above text boxes to enter an analysis configuration, you may save these settings by clicking the Save As button (Figures 4.6 and 4.7). This button allows you to save changes that you may have made with the User-Defined Settings. Associated with User-Defined settings above. Closes the Zone Analysis Select Definitions window. Exits the zone setup screen without incorporating any of the settings. Table Zone set up for data analysis 33

36 Rotational Behavior Calculations With the MED Rotational Analysis Setup, you can select from three pre-defined settings to analyze for large, medium, and small clockwise and counterclockwise rotations. We have also provided user-definable quadrant, radius and onset/backtrack-tolerance settings to provide flexibility for subject/treatment-specific analyses. The rotational analysis calculates the number of complete 360-degree revolutions for data analysis. The preset values analyze for small (Figure 4.10), medium (Figure 4.9), and large rotations (actually maximum radius), up to the entire diameter of the chamber (Figure 4.8). Remember, the OFA system tracks the center of the animal; therefore, the rotations are ambulatory circles, the path of which is defined by the radius, number of segments, and segment limits (forward and reverse). Bear in mind that rotations around the animal s center (i.e. rotations for chasing its tail) cannot be detected by this system. Figure Large rotational analysis (11.3 photo-beam interrupts) to for clockwise and counterclockwise movement. The Forward Limit has been set larger than the Reverse Limit in this example. 34

37 Figure Rotational Analysis for Medium radius (6.5 photo beams) Figure Rotational Analysis for Small radius (2.75 photo beams) 35

38 The Rotational Analysis Setup window has three display windows (Figures ) to customize rotational analysis configurations. The top left window displays the quadrant and maximum radius information to illustrate how modifications in these variables will affect analysis. A pie chart in the top right window displays the number of Segments, and this pie chart allows you to set "degrees of freedom" for the Forward Limit (red pie slices) and Reverse Limit (green pie slices). These settings tell the software when and how to record a rotation. The values used to set the Forward Limit allow you to measure either slow-moving or rapid rotations, and Reverse Limit parameters establish the conditions under which a new rotation is initiated. The following information is required to run Rotational Analysis: Item X Number Of Quadrants Y Number Of Quadrants Radius (number of photo beams) Segments Forward Limit Description Divides the chamber into the specified number of X quadrants. Setting the number of X and Y quadrants to 3 creates 4 intersections, or 4 independent areas within which rotational activity can be recorded. Each intersection will have a circle created around it, and the size of the circle is determined by Radius (see below). Greater numbers of X and Y quadrants translate into a greater area of the chamber Divides the chamber into the specified number of Y quadrants. Determines the size of the circle around each intersection. The animal must stay within the area of the circle for the rotation to be measured. Therefore, small radiuses will catch only small rotations or rotations that involve pivoting only, with no forwarddirectional ambulation. Large rotations will capture behavior that involves some forward-directional ambulation. Determines the resolution of the rotational analysis measurement. Selecting smallersized segments (greater overall number of segments) will allow for a more precise determination of forward and reverse movement (see Forward Limit, below). The Forward Limit determines how many Segments forward the animal is limited to move within one tick (50ms or the experiments resolution). For slow-moving rotational behavior, set the Forward limit to a small number (e.g. 1 Segment per 50ms), and faster rotations (> 1 Segment per 50ms) will be ignored. Ex: Segments is set to 8 and Forward Limit is set to 2. If the animal starts in Segment 1, it can safely move to Segments 2, 3 (clockwise rotation) or 8, 7 (counterclockwise rotation) and the program will continue to record the data until the subject has rotated 360 degrees and a Revolution is recorded. If the animal moves directly to Segment 5 by crossing the epicenter, the record resets since the animal has rotated more than the specified forward limit in one tick. Reverse Limit Determines how many segments in the reverse direction the animal can move before the reverse movement is considered a new rotation. Ex: Segments is set to 8, Forward Limit is set to 2, and Reverse Limit is set to 3. If the animal moves clockwise from Segment 1 into 2, the animal can then move counter-clockwise into Segments 1, 8, and 7, then move clockwise again. If the animal keeps moving counter-clockwise to Segment 6, then a new rotation is started from Segment 6 and the previous rotational movement is disregarded. 36

39 Item Pre-Defined Settings Description We have included three pre-defined settings for Large, Medium, and Small rotational behavior monitoring. The Large rotations settings are 17 x 17 quadrants, 11.3 Radius, 16 Segments, 5 Forward Limit segments, and 5 Reverse Limit segments. Medium rotations use a Radius of 6.5 photo beams. Small rotations use up to 2.75 photo beams in radius. User-Defined Settings Save As OK Cancel Like the Zone Analysis Definition window, the Rotational Behavior Analysis utility allows you to save customized settings as User-Defined (Figure 4.6). Associated with User-Defined settings above. Closes the Rotational Behaviors Select Definitions window. Exits the Rotational Behaviors setup screen without incorporating any of the settings. Table Rotational Analysis continued Using the Rotational Analysis Utility The preferred method of utilizing the Rotational Analysis is to compare the performance under control and experimental conditions. Use the exact same analysis parameters for both groups for the comparison. For example, ethanol intoxication might be evidenced by large rotations. To best assess the impact of ethanol exposure on activity, the radius should be large, the number of segments should be large, and the forward and reverse limit should be small. Rotational configuration in this manner will detect large, slow moving circles and allow comparisons to nontreated controls. Note that the radius is defined in photo-beam interruptions. In an ENV-510 chamber, the beams are spaced 5/8 of an inch apart. A radius of 6.5 photo beams is equivalent to 6.5 * 5/8 = inches. In an ENV-515 chamber, the beams are spaced 1 inch apart, so a radius of 6.5 beams would be equal to 6.5 inches. Save/Load Protocol After all of the Data Analysis Setup information has been entered, the established analysis protocol can be saved. This allows you to use the exact same settings to analyze all pertinent data sets by loading this protocol prior to data analysis. This protocol should be named such that the name represents the function. Loading the named protocol and clicking Analyze can expedite subsequent data-analysis sessions. Below is a graphic of the Data Playback Screen. You may analyze the data and view the subject plot in the process, or you may opt not to view (Figure 4.2, Table 4.1). 37

40 Figure Data Playback screen, analysis completed 38

41 Chapter 5 - Inserts for Open-Field Activity Dark Box Insert (Light/Dark Test) - Please note that inserts are not currently available for the VTI system. Dark Boxes are available for the mouse, ENV-511, and rat, ENV-516, sized activity chambers. The two-compartment Light/Dark Test (Light/Dark Conflict Test) is one of the classic indices of anxiety and is easily incorporated into the system while examining other components of locomotor activity. The Dark Box Insert is opaque to visible light and designed to cover 1/2 the area of the OFA Chamber. There is an opening into the Dark Box that allows the subject to pass freely, but is sufficiently small to minimize the amount of light that enters the darkened area. I/R Array height is the same as that for general open-field monitoring. The time spent in the light area or dark area, and entries into each zone, is determined using the Zone Analysis utility with two zones. A residual zone may be placed between the two zones to minimize artifact "bouncing" or "flickering" as a subject enters or leaves a zone. The residual zone can also be used to examine time-in-transition between the two zones. Match the two zones with the two areas of the Light/Dark test and analyze the data. Factory configured chambers are set up so that coordinate (0.5, 0.5) is at the opposite corner from the ENV-520 controller box and coordinate (16, 16) is in the same corner as the controller box. For complete instructions see Zone Analysis (Page 31). Figure Zone Analysis setup for the Light/Dark Insert. 39

42 Two Chamber Place Preference Two Chamber Place Preference is used for conditioned place preference paradigms. Like the Dark Box listed above, the Two Chamber Place Preference Insert is simply a box that slides into the chamber. After the box has been placed into the open-field environment you will need to adjust the I/R array heights to ensure that the subjects are tracked properly (Chapter 1, page 6, Modifying I/R Array Height). The two-chamber insert covers the entire area of the chamber. The outside of the box is constructed of clear polycarbonate. We have opted not to pattern the walls of the insert. Stickers, paper, or any easily removable material may be applied to the outside of these clear walls to provide distinct visual stimuli to maximize contextual differences; however, do not cover the photo beams. Each side of the box has a different floor, grid rods and/or wire mesh. The lid is hinged to allow easy subject insertion and removal. A manual guillotine door is provided that allows the subject to pass freely, if so desired. As described above, the software can parse the session data into zones and determine the amount of time that a subject spends in either area. Applications for this insert include two chamber Conditioned Place Preference tests and other two chamber contextual protocols. Two Chamber Place Preference Inserts are available for the mouse and rat sized chambers. Hole Board Task Floor The Hole Board Task has been used for over ten years as a spatial-orientation and learning test, a short-term and long-term memory test, and an attention and curiosity monitoring protocol/device. The Hole Board Task Floor insert is placed into the open-field activity arena. The Hole Board Floor insert has 16 holes (four rows of four, equidistant holes) with an underlying food tray. The I/R Arrays must be attached using the lowest available screw holes. This places the photo-beams between the floor and the tray to detect entries into the holes. Food may be placed into the tray for learning and memory protocols using working and reference memory ratios. A second, non-reward application is to simply place the animal on to the Hole Board insert and monitor hole entries for novelty/curiosity assessment. See Chapter 7 and Appendix VII for more information on using this insert. 40

43 Chapter 6 - Setting up an Ambulatory Experiment The preceding chapters have familiarized you with the hardware and software associated with your Open Field Activity System. These next two chapters will deal with how to set up, run, and analyze data. This chapter deals with running an ambulatory experiment using the OFA system alone or with either the Dark Box insert or the Place Preference insert. The following chapter will deal with how to run an experiment with the Hole Board insert. The first step we will be going over is configuring both the Preferences and the Experiment options. First go to File Configuration Preferences: Figure Preferences Menu Item For the purpose of this example experiment, we will use the ENV-515 that is equipped with 16 beam arrays. We will demonstrate how to generate summary files, automatically name files, and start on animal entry. The same configuration will also be used for other examples in this chapter 1. When your screen looks like this one below, click OK: Figure Preferences Screen 1 When using a mouse chamber set the chamber to ENV-510, but keep all other settings the same. 41

44 Next we will configure the experiment, so please go to File Configuration Experiment and select the following (If you have any questions about any of the items on this screen, please refer to pages 12 to 16): Figure Configuration Screen When the preceding information has been entered, please click on the Save As button and save it as TEST.CFG 2 Now go to Run Open Experiment. Enter the following on the screen: Figure Screen that Loads/Starts Experiment Please note, make sure that Start Box is checked and then select the OK button. 2 By saving this file as TEST.CFG, the naming of files will remain constant throughout this chapter. When setting up a standard experiment MED Associates recommends saving the experiment as the default (DEFAULT.CFG). This ensures that the standard experiment is ready to run when Activity Monitor is started. 42

45 If everything was done correctly, nothing should be happening and the screen should look like this: Figure Run Time Screen in wait mode. Although we selected to start the box, we also configured the chamber to start collecting data upon animal entry. The purple light at the bottom-right hand corner of the screen signifies that the box is loaded and awaiting an animal. At this time, place an animal into the chamber and the screen should look like this: 43

46 Figure Run Time Screen as Experiment Runs Allow the experiment to run its course. When the designated time is up, in this case three minutes, the program will stop collecting data and the plot will stop moving with the animal, despite the fact that the animal is still moving. If you now go to Run Close Experiment the following screen will appear: Click Yes to exit the run time screen. Figure Close Experiment Pop Up 44

47 Now we are ready to analyze the data we have collected. Go to File Data Analysis. A screen similar the following will appear: Figure Data Analysis Database Window The top half of the screen shows all of the available experimental databases available. The bottom half are subject data, sorted by ID. After clicking on the Test - Config row on the top half, select the proper subject on the bottom half. Clicking the row of the subject you want to analyze does this. Since we only have one subject listed, this is a moot point. Figure Data Analysis Option Screen Above we see the Data Analysis screen. Before proceeding, make sure that all boxes in the lower left hand corner are X ed as this will allow you to see all of the features of the Data Analysis portion of your software. Since we have already set up the information under the General section when we configured our experiment (Figure 6.3), we will leave it as is. Go ahead and click on Select Definition under Zone Calculations. 45

48 Figure Zonal Analysis Screen For the purpose of this demonstration, we will use the predefined Quadrants zonal analysis. If you were running a light/dark box insert, or a place preference insert, you would want to make sure that you collect data that would be distinctly in either one side or the other. In this case, you would want to use the following configuration, making sure to click Save As not only to save your user defined changes, but also to see the changes on the screen: Figure Example of Custom Zonal Analysis Screen If you have questions on anything on this screen, refer to the zone analysis section in chapter four for definitions and explanations, if not click OK. 46

49 Click Select Definition under Rotational Calculations on the main data analysis window. Figure Rotational Analysis Screen For the purpose of this demonstration, we will be looking at small rotations, using the defined radius, segments, and limits shown above. If you have questions on anything on this screen, refer to pages for definitions and explanations, if not click OK. 47

50 Now we are ready to click Analyze on the main data analysis window. Figure Analysis Screen The above screen is the post analysis screen and shows all the data collected and chose to analyze (e.g., revolutions and zonal entries). Clicking on Previous or Next will let you cycle between each of the one-minute blocks we defined and see how the data varied. To see the summary file that was created when the experiment was first run, Use a text editor or spreadsheet program (e.g. Notepad or Excel), and from your data directory (C:\Program Files\Activity) open the file: Subject_123_Group_321_Experiment_Test-Config.Summary To see the zone analysis file that was just created, open the file: Subject_123_Group_321_Experiment_Test-Config.Zone We also selected to save our file in the database (ANALYSIS.MDB); so all data can be opened with a database. 48

51 Chapter 7 - Setting up a Hole Board Experiment Note: The Hole Board Floor Insert is not supported by the VTI system. Like with the ambulatory experiment in the preceding chapter, the first step we will be going over is configuring both the preferences and the experiment. First go to click File Configuration Preferences: Figure Menu Options for Set Up Once again, we will be using the ENV for the purposes of this example experiment. When your screen looks like this one below, click OK: Figure Preference Screen 49

52 Next we will configure the experiment, so please go to File Configuration Experiment and select the following. Figure Configuration Screen Since we are running a hole-board experiment and measuring nose-poke behavior, we must check Hole Board Floor Installed. Check Hole Board Strips Installed to monitor both activity and nose-poke behavior. The hole-board strips plug into the Z-axis I/R-array strips. Next, click on Define Task Floor. Enter the following information. Figure Baited Hole Selection Screen 50

53 To tell the program which holes are baited, just click on the appropriate hole. When the computer registers that the selection has been made, the circle color will turn red. If you inadvertently select the wrong hole, click it a second time to deselect it. After the four holes listed have been selected, turn on the option Terminate On Completion of Task and then please click the OK button. At the main Experimental Configuration window, click on the Save As button and save it as HOLEBOARD.CFG. Now go to Run Open Experiment. Enter the following on the screen: Figure Start Hole Board Experiment Screen Please note, make sure the Start Box is clicked and now select OK. If everything was done correctly, nothing should be happening and the screen should look like this (see the next page): 51

54 Figure Run Time Screen at Start Test the system by placing objects into the holes and notice how the counts are incremented on the screen, like so: Figure Run Time Screen while Experiment Runs 52

55 Allow the experiment to run its course (i.e. trigger all four baited holes). At this point you may go to Run Close experiment. Click Yes. Figure Close Experiment Pop Up With Activity Monitor 5.1 you can do a Data Analysis of your saved data. With previous versions you need to have the hole-board strips installed in order to do a Data Analysis. To do a Data Analysis go to File Data Analysis. A screen similar to the following will appear: Figure Hole Board Data Set Selection Screen The top half of the screen shows all of the available experimental databases available. The bottom half list the subjects, sorted by ID. After clicking on the row on the top half, select the proper subject on the bottom half. Clicking the row of the subject you want to analyze does this: Figure Data Analysis Option Screen 53

56 Before proceeding with data analysis, make sure that all boxes in the lower left hand corner are checked because this will allow you to see all of the features of the Data Analysis portion of your software. For the hole-board experiment we are going to leave all options at their default values, so just click on the button that says Analyze to go to the main data analysis window. Figure Analysis Screen The above screen is the post analysis screen for hole-board data. The red circles indicate the selected task holes, the green numbers indicate entries into the task holes, the yellow numbers indicate entries into non-task holes, and the solid red circle indicate repeated entries into a task hole. If you have the hole-board strips installed, then the screen can also show zonal and revolution data. Clicking on Previous or Next will let you cycle between each block; however, since we only defined one three-minute block, the data will not change. To see the summary file that was created when the experiment was first run, go to your data directory (unless it was changed, it will be C:\Program Files\Activity) and open the following file in a text editor (e.g. Notepad): Subject_555_Group_222_Experiment_ Summary To see the zone analysis file that was just created, open the file: Subject_555_Group_222_Experiment_ Zone We also selected to save our file in the database (ANALYSIS.MDB); so all data can be opened with a database. 54

57 File Naming Appendix I - File Naming and File Types The OFA system program automatically generates a file name based upon the Experiment ID, Subject ID, and Group ID entered into the Run Experiment setup and run screen. There are four types of data files, three are ASCII text files and the fourth is the database files, with linked data contained in EXP.MDB and ANALYSIS.MDB. Summary data files contain a SUMMARY extension like the following: Subject_1_Group_1_Experiment_1.Summary Exporting data generates a Subject_1_Group_1_Experiment_1.Export filename. Analyzed data files are named Subject_1_Group_1_Experiment_1.Zone. File Types Figure A1.1 - File Types Above are the file types used with the Activity Monitor system. From top to bottom, the file types are as follows: 55

58 1. Data subdirectory. It is a good idea to store your data in a separate folder. 2. ActivDll.dll. Library file used by the Activity program. 3. Activity.exe. The executable file that runs the show. 4. Activity.hlp. The on-line help file. 5. Activity.ini. Configuration file used to save the User Preferences. 6. Analysis.ldb. This file contains instructions for Analysis.mdb. 7. Analysis.mdb. This file contains the analyzed data in a database. 8. Default.cfg. This file contains the experiment specific parameters required to sample and process data during acquisition. 9. Default.pro. This is an analysis profile that contains the instructions needed by the software to do a specific, saved, and defined (by the user) analysis of the data. 10. Default.zip. THIS IS THE MOST IMPORTANT FILE IN THE ACTIVITY DIRECTORY. THIS FILE CONTAINS ALL OF THE RAW DATA THAT WAS RECORDED DURING THE EXPERIMENTS. BACKUP THIS FILE OFTEN. Within this file is a A01 - *.Z99 file for every subject run or imported. This name denotes month, day, year, and a unique identifier suffix (A01 - Z99). If you ran 10 subjects, three times a day for 3 days, you would have three sets of files with the same month, day, year.a01 - A30. The information necessary for the software to discern which animal the file relates to in the file itself. 11. Exp.ldb. This file contains instructions for Exp.mdb. 12. Exp.mdb. This is the database file created the very first time that you enter an experiment, run a few subjects and close that session. Within this file are all of the pertinent header categories, summary data, block data, and specific session file ID's that link everything together. This information is linked to the analyzed data information in Analysis.mdb via Subject ID, etc. It is pretty straightforward and fairly simple to cross tabulate; however, it may be more efficacious to perform SQL queries, which could require some programming help. 13. Exp.wid. This file contains the instructions that define the column widths for the various tabular screens. 14. Subject_123_Group_321_Experiment_Test-Config.Summary. This file is a summary data file for Subject 123 of Group 321 in Experiment Test-Config. 15. Subject_123_Group_321_Experiment_Test-Config.Zone. This is an analyzed data file for Subject 123 of Group 321 in Experiment Test-Config. Any time that an analysis is done on this subject s data, it is appended to the same file. 56

59 Summary Data Appendix II - Available Data The summary data filenames end with the SUMMARY extension. Summary data files can use either the Relative or Absolute data formats. Both formats are shown below. Printed : 09/03/ :28:34 Activity Summary, 5.10 ================ Experiment Title Experiment Comment : Sample Test : This is only a test Resolution (ms) : 50 Box Size : 4 Resting Delay (ms) : 500 Ambulatory Trigger : 3 Session Type : C Session Time (min) : 3 Actual Run Time : 003:00.00 Data Save Interval (sec) : 60 Start on Animal Entry : Yes Raw Filename : C0 Chamber Number : 1 Chamber Type : ENV Units : Cm Hole Board Installed Session Comment : No : This is the first trial Subject ID : 123 Experiment ID : Test - Config Group ID : 321 Session No : 1 Data Filename : Subject_123_Group_321_Experiment_Test-Config.Summary Start Date : 9/3/03 Start Time : 10:25:29 Detail Reporting Mode : Absolute Dist. Time Amb. Time Ster. Time Vert. Vert. Session Trav. Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Time ======= ========= ====== ========= ====== ========= ====== ========= ========= : : : : : : : : : : : : : : :00.00 Jump Jump Average Ambulatory Session Counts Time Velocity Episodes Time ======= ========= ========== ========== ========= 0 000: : : : : :

60 Printed : 09/03/ :28:34 Activity Summary, 5.10 ================ Experiment Title Experiment Comment : Sample Test : This is only a test Resolution (ms) : 50 Box Size : 4 Resting Delay (ms) : 500 Ambulatory Trigger : 3 Session Type : C Session Time (min) : 3 Actual Run Time : 003:00.00 Data Save Interval (sec) : 60 Start on Animal Entry : Yes Raw Filename : C0 Chamber Number : 1 Chamber Type : ENV Units : Cm Hole Board Installed Session Comment : No : This is the first trial Subject ID : 123 Experiment ID : Test - Config Group ID : 321 Session No : 1 Data Filename : Subject_123_Group_321_Experiment_Test-Config.Summary Start Date : 9/3/03 Start Time : 10:25:29 Detail Reporting Mode : Relative Dist. Time Amb. Time Ster. Time Vert. Vert. Session Trav. Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Time ======= ========= ====== ========= ====== ========= ====== ========= ========= : : : : : : : : : : : : : : :00.00 Jump Jump Average Ambulatory Session Counts Time Velocity Episodes Time ======= ========= ========== ========== ========= 0 000: : : : : :00.00 ============================================================================================== Distance Traveled : Time Ambulatory :000:16.95 Ambulatory Count : 181 Time Stereotypic :000:32.60 Stereotypic Count : 374 Time Resting :002:05.95 Vertical Count : 192 Time Vertical :000:51.80 Jump Count : 4 Time Jumping :000:04.50 Average Velocity : Ambulatory Episodes : 23 58

61 Summary data files contain the following measures: Measure (pre-analysis) Dist. Trav. (Cm or In - User-definable) Time Amb. (Sec) Amb. Cnts. Time Ster. (Sec) Ster. Cnts. Time Rest. (Sec) Vert. Cnts. Vert. Time (Sec) Session Time Jump Counts Jump Time (Sec.) Average Velocity (Cm/Sec or In/Sec) Definition (Data are presented in block intervals and session totals) Distance traveled is defined by the combination of Box Size and Resting Delay parameters. This creates a threshold, and the subject must move a specified distance (Box Size) in a defined period of time (Resting Delay) to maintain ambulatory movement status. Time the subject spends in ambulatory movement status. The time and distance (above) are used to determine velocity. The number of photo beam breaks (counts) while in ambulatory movement status. Time spent breaking beams while staying inside the Box. Total number of beam breaks while staying inside the Box. When the animal leaves the Box, it is considered an Ambulatory Episode and beam breaks are no longer counted as Stereotypic. When the animal then stops for an amount of time equal to the resting delay, a new Box based around the animals current position is established and beam breaks are once again counted as Stereotypic. Time spent with no new beam breaks. Number of periods of continuous beam breaks reported by the "Z" I/R Array strips. Total time breaking "Z" beams. Total session time If a subject jumps and he leaves the photo-beam array for a period of time, the software records 0,0 s for that period of time. The number of continuous 0,0 records will be counted. If the "X" & "Y" I/R Array strips have not been well centered on the subject, there may be error in this data (Chapter 1, Modifying I/R Array Height). Time spent with 0,0 coordinates, which indicate a jump, under the beams or standing against the wall with all photo-beams passing through their legs. Use care when adjusting the photo-beam array heights. The average velocity for each data block and total for the session. This measure may be very useful for establishing the criteria by which Box Size and Resting Delay times may be set. See Appendix IV for additional information. Ambulatory Episodes The number of times that the subject leaves the Box and travels beyond the user-defined ambulatory trigger (number of photo beams) before the resting delay criteria is fulfilled. Hole Board Data See Table A2.3. Table A2.1 - Summary Data 59

62 Analyzed Data The analyzed data filenames end with the ZONE extension. Analyzed data files can use either the Relative or Absolute data formats. Both formats are shown below. 09/03/ :47:39 Activity Zone Analysis, 5.10 ====================== Experiment Title: Sample Test Experiment Comment: This is only a test Number of Test Chambers: 1 Resolution (ms): 50 Box Size: 4 Resting Delay (ms): 500 Session Time (min): 3 Data Directory Name: C:\PROGRAM FILES\ACTIVITY MONITOR\DATA\ Raw Data File: C0 Text Data File: Subject_123_Group_321_Experiment_Test-Config.Zone Chamber Type: ENV Units: Cm Chamber Number: 1 Session Comment: This is the first trial Subject ID: 123 Experiment ID: Test - Config Group ID: 321 Session No: 1 Start: 9/3/03 10:25:29 Start Time Displayed (mins): 000:00.00 End Time Displayed (mins): 003:00.00 Block Time (secs): 60 Detail Reporting Mode: Absolute Rotational Analysis Number Of Quadrants X: 17 Y: 17 Valid Radius: 2.75 Segments: 16 Segment Limit: 5 Reverse Limit: 5 Counter Clockwise Clockwise Block Block Block

63 Zones Defined Start X Start Y End X End Y Zone Zone Zone Zone Zone 1 (0.5, 0.5) to (8, 8) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : : Zone 2 (8, 0.5) to (16, 8) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : : Zone 3 (0.5, 8) to (8, 16) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : : Zone 4 (8, 8) to (16, 16) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : :

64 Zone Totals Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : : : : : : :34.45 ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : Block Summary Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Trav.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries ========== ========= ====== ========= ====== ========= ====== ========= ========== : : : : : : : : : : : : Block Summary (Cont) Jump Jump Average Ambulatory Session Counts Time Velocity(cm/s) Episodes Time ========== ========= ============== ========== ========= 0 000: : : : : :

65 09/03/ :48:29 Activity Zone Analysis, 5.10 ====================== Experiment Title: Sample Test Experiment Comment: This is only a test Number of Test Chambers: 1 Resolution (ms): 50 Box Size: 4 Resting Delay (ms): 500 Session Time (min): 3 Data Directory Name: C:\PROGRAM FILES\ACTIVITY MONITOR\DATA\ Raw Data File: C0 Text Data File: Subject_123_Group_321_Experiment_Test-Config.Zone Chamber Type: ENV Units: Cm Chamber Number: 1 Session Comment: This is the first trial Subject ID: 123 Experiment ID: Test - Config Group ID: 321 Session No: 1 Start: 9/3/03 10:25:29 Start Time Displayed (mins): 000:00.00 End Time Displayed (mins): 003:00.00 Block Time (secs): 60 Detail Reporting Mode: Relative Rotational Analysis Number Of Quadrants X: 17 Y: 17 Valid Radius: 2.75 Segments: 16 Segment Limit: 5 Reverse Limit: 5 Counter Clockwise Clockwise Block Block Block Total

66 Zones Defined Start X Start Y End X End Y Zone Zone Zone Zone Zone 1 (0.5, 0.5) to (8, 8) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : :15.45 ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : Zone 2 (8, 0.5) to (16, 8) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : :30.05 ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : Zone 3 (0.5, 8) to (8, 16) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : :04.10 ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : Zone 4 (8, 8) to (16, 16) Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : :10.40 ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : :

67 Zone Totals Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Zone Tr.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries Time ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : : : : : : : : : : : : : : : :34.45 ======= ========= ====== ========= ====== ========= ====== ========= ========== ========= : : : : : Block Summary Dist. Time Amb. Time Ster. Time Vert. Vert. Zone Trav.(cm) Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Entries ========== ========= ====== ========= ====== ========= ====== ========= ========== : : : : : : : : : : : : ========== ========= ====== ========= ====== ========= ====== ========= ========== : : : : Block Summary (Cont) Jump Jump Average Ambulatory Session Counts Time Velocity(cm/s) Episodes Time ========== ========= ============== ========== ========= 0 000: : : : : :00.00 ========== ========= ============== ========== ========= 4 000: :00.00 The data analysis file contains the first 13 measures listed in the summary data table (A2.1) above plus the following measures: Definition Measure (Data may be presented in block intervals by zone with zone and session totals) Rotational Analysis Maximum radius is user definable. Rotations are presented as clockwise and counterclockwise counts. Zone Entries Zone Time The number of times the animal entered the zone from a different zone. Amount of time the animal is present in each zone. Table A2.2 - Analyzed Data Note: All data may be re-analyzed using different parameters, so make sure that you are using the same measures when performing your statistical analysis. 65

68 Hole Board Task Data The hole-board data filenames end with the SUMMARY extension. If you have hole board strips installed, then the hole-board data files may contain block information with either the Relative or Absolute data formats, just like a regular summary data file. Below is an example of a holeboard data file without hole-board strips installed and with hole-board strips installed. Printed : 09/02/ :19:18 Activity Summary, 5.10 ================ Experiment Title : Hole Board Test Experiment Comment : Just a test Resolution (ms) : 50 Box Size : 3 Resting Delay (ms) : 500 Ambulatory Trigger : 3 Session Type : C Session Time (min) : 3 Actual Run Time : 001:15.95 Data Save Interval (sec) : 180 Start on Animal Entry : No Raw Filename : D0 Chamber Number : 1 Chamber Type : ENV Units : Cm Hole Board Installed : Yes Terminate on Task Completion: Yes Hole Board Strips Installed : Yes Task Holes : 1, 7, 9, 15 Session Comment : None Subject ID : 555 Experiment ID : Group ID : 222 Session No : 1 Data Filename : Subject_555_Group_222_Experiment_ Summary Start Date : 9/2/03 Start Time : 11:18:02 Total Session Time : 001:15.95 Task Complete Time : 001:15.60 Latency To First Hole : 000:17.15 Novel Task Entries : 4 Novel NonTask Entries : 6 Novel Entries : 10 Repeat Task Entries : 1 Repeat NonTask Entries: 7 Repeat Entries : 8 Total Entries : 18 Avg. Novel Task IRT : Avg. Novel NonTask IRT: 5.37 Avg. Novel Total IRT : 6.48 Working Memory Ratio : 0.80 Reference Memory Ratio:

69 Printed : 09/02/ :19:18 Activity Summary, 5.10 ================ Experiment Title Experiment Comment : Hole Board Test : Just a test Resolution (ms) : 50 Box Size : 3 Resting Delay (ms) : 500 Ambulatory Trigger : 3 Session Type : C Session Time (min) : 3 Actual Run Time : 001:15.95 Data Save Interval (sec) : 180 Start on Animal Entry : No Raw Filename : D0 Chamber Number : 1 Chamber Type : ENV Units : Cm Hole Board Installed : Yes Terminate on Task Completion: Yes Hole Board Strips Installed : Yes Task Holes : 1, 7, 9, 15 Session Comment : None Subject ID : 555 Experiment ID : Group ID : 222 Session No : 1 Data Filename : Subject_555_Group_222_Experiment_ Summary Start Date : 9/2/03 Start Time : 11:18:02 Detail Reporting Mode : Absolute Dist. Time Amb. Time Ster. Time Vert. Vert. Session Trav. Amb. Cnts. Ster. Cnts. Rest. Cnts. Time Time ======= ========= ====== ========= ====== ========= ====== ========= ========= : : : : :15.95 Jump Jump Average Ambulatory Session Counts Time Velocity Episodes Time ======= ========= ========== ========== ========= : :15.95 Total Session Time : 001:15.95 Task Complete Time : 001:15.60 Latency To First Hole : 000:17.15 Novel Task Entries : 4 Novel NonTask Entries : 6 Novel Entries : 10 Repeat Task Entries : 1 Repeat NonTask Entries: 7 Repeat Entries : 8 Total Entries : 18 67

70 Avg. Novel Task IRT : Avg. Novel NonTask IRT: 5.37 Avg. Novel Total IRT : 6.48 Working Memory Ratio : 0.80 Reference Memory Ratio: 0.28 The hole board data file contains the first 13 measures listed in the summary data table (A2.1) above plus the following measures: Measure Total Session Time Task Completion Time Latency to First Hole Novel Task Entries Novel NonTask Entries Novel Entries Repeat Task Entries Repeat Non-Task Entries Repeat Entries Total Entries Avg. Novel Task IRT Avg. Novel NonTask IRT Avg. Novel Total IRT Working Memory Ratio Reference Memory Ratio Definition The time necessary to run the session. This may be the task completion time or the session limit time depending upon the setup. Time to enter all of the user-defined (task) holes. The time elapsed between starting the experiment and entry into the first hole. Total task holes entered at least once. Total non-task holes entered at least once. Entering a hole for the first time. Total re-entries into task holes. Total re-entries into non-task holes. Each subsequent entry after a novel entry. These can be task or non-task holes. The total number of entries for an entire session. Average time between novel task hole entries. Average time between novel non-task hole entries. Average time between total hole entries. The number of novel entries into baited holes divided by the number of entries and re-entries into baited holes. The number of entries and re-entries into the baited holes divided by the total number of entries into baited and non-baited holes. Table A2.3 - Hole Board data 68

71 Exported Raw Data Files The exported data filenames end with the EXPORT extension. The data files contain the raw data that was recorded when the experiment was first run. The raw data can be exported in the Annotated or Stripped format. Examples of both are given below. Annotated Experiment Title: Sample Test Experiment Comment: This is only a test Number of Test Chambers: 1 Resolution (ms): 50 Box Size: 4 Resting Delay (ms): 500 Session Type: C Session Time (min): 3 Hole Board Installed: No Data Save Interval (sec): 60 Data Save Mode: R Raw Data Filename: C0 Chamber Number: 1 Session Comment: This is the first trial Subject ID: 123 Experiment ID: Test - Config Group ID: 321 Text Data Filename: Subject_123_Group_321_Experiment_Test-Config.Summary Start Date: 09/03/2003 Start Time: 10:25:29 Time X Y Z ========= ===== ===== ===== 000: : : : : : : : : : : :

72 Stripped 000: : : : : : : : : : : :

73 Appendix III - Importing information from the ANALYSIS.MDB database into Excel Start Microsoft Excel. Go to Data Get External Data New Database Query as shown in Figure A3.1 Figure A3.1 - New Database Query Select MS Access Database from the list of databases as shown in Figure A3.2, and click the OK button. Figure A3.2 - Choose Data Source 71

74 Go to your Activity directory and select the ANALYSIS.MDB database as shown in Figure A3.3. Figure A3.3 - Select Database Click on the table of data that you want to include in your query and then click the OK button. Refer to Figure A3.4. If you aren t sure, include them all. Undesired fields may be deleted later. Figure A3.4 - Query Wizard After including the last desired table, click the Next button. See Figure A3.5 72

75 Figure A3.5 - Query Wizard with Selected Columns You will receive a message as shown in Figure A3.6. Click the OK button. Figure A3.6 - Microsoft Query Message The Microsoft Query form will display as shown in Figure A3.7 73

76 Figure A3.7 Microsoft Query from MS Access Database Select the ID field in the Header table. Drag it to the ID field in the Blocks table. Then drag the ID field from the Header table to the ID field in the Hole Board Data table. Then drag the ID field from the Header table to ID field in the Latencies table. Finally drag the ID field from the Header table to the ID field in the Zones table. Refer to Figure A3.8 74

77 Figure A3.8 - Linking ID Fields Select the Block No field in the Blocks table. Drag it to the Block No field in the Zones table. Refer to Figure A

78 Figure A3.9 - Linking Block No Fields In a Query you can delete unwanted columns as shown in Figure A

79 Figure A Removing Unwanted Columns from the Query You can also move columns around by clicking once on its header and then when the entire column is highlighted dragging it to the desired location. Once your query is setup as desired, save it by going to File Save as shown in Figure A

80 Figure A Save the Query By saving the Query, you will be able to rerun it in Excel at a later date, with a new Analysis database. The only time you will need to go through these steps again is if you wish to modify the data fields returned to Excel. Select File Return Data to Microsoft Excel to exit the query form as shown in Figure A

81 Figure A Return Data to Microsoft Excel Excel will prompt you as shown in Figure A3.13 for where to place the returned data. Figure A Returning External Data to Microsoft Excel Figure A3.14 shows what the returned data will look like in Excel. 79

82 Figure A Queried Data in Excel from MS Access Database To run your saved query go to Data Get External Data Run Saved Query as shown in Figure A3.15. Figure A Run Saved Query 80

83 Select your saved query as shown in Figure A3.16 and click on the Get Data button. Figure A Selecting Saved Query to Run 81

84 Appendix IV - Using Box Size, Resting Delay, Include Resting Delay, and Ambulatory Trigger Defining Distance Traveled Box Size is the User-defined number of X or Y photo-beams that need to be broken before a movement is considered ambulatory. Starting at time 0, the Box is centered on the subject. When the animal moves from within the Box to outside the Box, it is considered ambulatory and the Box re-centers on the subject. The subject remains ambulatory until it does not leave the last re-centered Box in less than the Resting Delay. Ambulatory Time, Counts, and Distance Traveled are then calculated. If the subject travels equal to or further than the Ambulatory Trigger during the time prior to the fulfillment of the Resting Delay, then this constitutes one Ambulatory Episode and velocity is calculated. The Ambulatory Distance measure includes the distance from the end of the last ambulatory movement episode (time 0, or the last episode wherein the subject did not exit the Box in less than the Resting Delay) to the end of the subsequent ambulatory episode. For example, Figure A4.1 represents a 2-beam Box with a subject making 5 movements within the Box and 2 outside. Figure A4.1 - Include Resting Delay distance. The pictured dots represent photo beams and each grid represents ½ of a photo beam (the software resolution). Each arrow with a corresponding number represents a subject movement. The dashed arrow is the transition movement to ambulatory and the dashed box is the re-centered box. The dark arrow is the last subject movement and C E and BB and the beams broken during the ambulatory movement. 82

85 Only the distance from X to 6 (the dashed line) is used to determine Distance Traveled. In this manner, movements within the Box are eliminated, thus providing a "filtered" Distance Traveled measure. At 6 above, the Box re-centers on the subject. If the subject moves through the next Box in less than the Resting Delay, the ambulatory Distance Traveled is the distance from X to 6 + the distance to 7. The number of X + Y photo beam breaks that occurred is the Ambulatory Count. Ambulatory Time is defined as the time from leaving the first Box, until the time that the subject enters the last Box and does not leave in less than the Resting Delay. And this all occurs in one Ambulatory Episode. If data are parsed into time blocks, an Ambulatory Episode and its associated velocity is only logged in the block in which it ends. Ambulatory Distance Traveled is logged across time blocks, however. Distance Traveled is modified if Include Resting Delay is activated. If the animal moves from X to 1, 2, 3, 4, 5 and then 6 before the Resting Delay has elapsed, the sum of all movements (distances) from X through 6 is used to determine the Distance Traveled. If the Resting Delay times-out prior to the subject leaving the Box, then the distance from X to 6 is used to determine the Distance Traveled. This measure has been included to allow for consistency with other systems that do not have this "filtering." The Ambulatory Trigger number adds an additional variable. This number represents the minimum total X + Y beam breaks that must occur to be considered an Ambulatory Episode. The beams must be broken before the Box times-out in order for the Ambulatory Episode and velocity for that given episode to be acquired. In Figure A4.1, A - D and AA are the beams broken after leaving the box and during a continuous movement of two user-defined sample times (resolution). An Ambulatory Trigger of 4 or less would enable measures 1 and 2 (above) to be determined. The Ambulatory Trigger is useful if you are trying to generate a velocity measure that enables you to determine a Box Size and Resting Delay to differentiate between large/quick and small/slow movements (below). The Ambulatory Trigger can also be used to further define the onset of an ambulatory episode, beyond Box Size and Resting Delay, as continuous. Differentiating Between Large/Quick and Small/Slow Movements Given the Box Size, Resting Delay, and Ambulatory Trigger functions described above, it is possible to differentiate groups of subjects based upon their types of movements. The defining measures would be Ambulatory Time, Ambulatory Counts, Ambulatory Episodes, Average Velocity, and Distance Traveled. Let's assume that we have two groups of subjects, one control group (C) and one loco-motor impaired group. The loco-motor impaired group is a Parkinsonian group (P), for example. If we were to measure Distance Traveled between the two groups, C's may move 1000 cm in 20 minutes with periods of quick movements (high velocity) and periods of minimal movements (resting or stereotypic). Within a 20-minute period, P's may also move 1000 cm with few, if any, fast movements but continuous slow movements. As you can see, Distance Traveled may not accurately depict between-group differences in loco-motor activity. 83

86 The Box Size and the Resting Delay combine to create a threshold whereby a subject must move a certain distance (Box Size) in a maximum amount of time (Resting Delay) to maintain its ambulatory status. By determining a Box Size large enough for C's to leave in an amount of time (Resting Delay) that P's cannot, you may be able to differentiate the groups by analyzing for Ambulatory Times and Counts. 84

87 Appendix V - Multiple Users To setup Activity Monitor v5.2 and higher so that multiple users can have their own database of experiments, you must perform the following steps: 1. Create the new data directories. For the sake of demonstration, we will say the directory names are C:\LAB1 and C:\LAB2 2. Right click on the activity.exe file in your Activity Monitor folder. Highlight and click on Send To Desktop (create shortcut). 3. Create as many shortcuts as you have new data directories (in our example, two) 4. Right click on one of the shortcuts that you just created and select Properties 5. Change the Target box from C:\Program Files\Activity Monitor\Activity.exe to read C:\Program Files\Activity Monitor\Activity.exe LAB1 (Figure A5.2). Figure A5.1 - Right Click Menu for Activity Monitor Shortcut Shortcut LAB1 will be the name of the INI file that will store all of your Activity Monitor preferences including the Data Directory. There can be no spaces in the file name. Make the same change to each shortcut that you created. Figure A5.2 - Properties of Activity Monitor 85