M-Series (BAS) Geolocators Short Manual

Transcription

1 M-Series (BAS) Geolocators Short Manual Communicating with M-SERIES geolocators...2 Starting recording...3 Pre- and Post-Calibration (Ground Truthing)...4 Deployment...5 Download...7 Appendix 1 - Linux and Mac OS...10 Appendix 2 reasons for poor connection...10 Introduction You have now received your tags and they must be started and deployed before putting on the birds. M-Series geolocators are supplied in SLEEP mode and must be started before deploying, otherwise no data will be recorded. This guide is a shortened summary of the Main Manual. We have tried to keep it as brief as possible, so that you can start using your tags quickly. However, there is more useful information in the Appendices here and the Main Manual, so please refer to those as well for a more complete explanation of these geolocators M-Series Geolocators are based on devices developed by the British Antarctic Survey, now produced by Biotrack Ltd.

2 Communicating with M-SERIES geolocators You require: PC/Laptop running Windows OS (for Mac or Linux see Appendix 1) CD for installing software Interface box - When not using the interface, connect the red and black clips together to minimise risk of static damage. First Install the software from the CD. Click on install.bat Now connect your interface box to the computer using the USB lead supplied. If it is the first time you have connected then give Windows time to identify the new hardware device and establish the driver for it. Wait for the popup message saying that your new hardware is ready to use. Establish which COM port you are using. If you run the BASTrak Communicate program then the COM port will probably be the highest number from the drop down list. You may need to establish the COM port number from Windows Device Manager (Start -> Control Panel -> System -> Hardware -> Device Manager -> Ports for XP); the interface box may be listed as USB Serial Port. A little trial and error may be needed at first. Pressing enter or, with Communicate, clicking on the press enter button should elicit a response from the interface box when working correctly. Select the COM port you have established that you are using. You will get a window asking for Port settings. Use the following values: Bits per second (also known as baud rate): 9600 Data bits: 8 Parity: None (or N) Stop bits: 1 Flow control: None (or N) Follow the instructions that appear in the communication window and connect a geolocator. If there is no response, or you find you get a BAD CONNECTION message then try swapping the clips, cleaning the terminals or reconnecting the clips to improve the contact. See Appendix 2. Please note that with smaller versions of our M-Series tags, you will have to wait up to a minute before a successful connection message is returned. If, at any time, the screen freezes or no instructions appear, try first disconnecting and then reconnecting the interface box from the end of the cable. You will need to exit or restart BASTrak Communicate

3 Starting recording M-Series geolocators have two modes: Sleep: this uses 20% less battery and does not use up memory Recording: must be in this mode to record light data Make sure your geolocator is recording before deployment You do not need to start the geolocators in the field; due to their long life, they can be started many days before deployment. Recording is started by communicating with the interface box and answering the questions asked by the interface software. [Press y ] to start the tag. [Press n ] to RECEIVE THE DATA [Press n ] to STOP COLLECTING When you start RECORDING, and download data, you MUST make a note of the time see Deployment below. An absolute time reference is not recorded by the geolocator; accuracy to the nearest minute is acceptable. There is no way of knowing if the geolocator is RECORDING other than by communicating with the unit. If you ever want to check, connect to the geolocator using the interface box. It will tell you the mode and, if recording, how long it has been recording. It would be a good idea to look at the data after Pre-Calibration (if not on the animal) to check progress.

4 Pre- and Post-Calibration (Ground Truthing) If you have time before putting the geolocators on your target animals then you should perform a Pre-Calibration with every geolocator. Individual variations in the units may cause slight variation in light level sensitivity and calibration of sensitivity is also necessary to compensate for habitat shading (through foliage or cloud, for example). If possible a Post-Calibration should also be carried out after retrieving the tag, but there is a chance the battery will have finished, so the Pre-Calibration is very important. Aim: to identify the light level that corresponds to a certain sun elevation for post-processing the data. This is best if the environment mimics the environment experienced by the animal. Options (from best to worst): 1. Put on animal that stays in the area for at least a week prior to migration, and uses similar habitat (w.r.t. shading) as when on migration. NB when using cavities this data will be inappropriate. 2. Leave for at least a week in stationary location, with similar habitat (w.r.t. shading) as when on migration. 3. Put out in the open for at least a week. In all cases make sure that the light sensor has the best situation to capture all the daylight. Make a written record of when you put geolocators out, when you remove them and the location latitude and longitude of the calibration site (+/ degrees). see Deployment for comprehensive list. Also, it is beneficial to keep a record of the cloud cover and weather conditions at times of dawn and dusk at the chosen location over the calibration period. Noting snowfall events or heavy frost during this period is important along with anything else occurring which may obscure the light sensor at dusk or dawn. This information can be used later during analysis and, at the very least, will familiarise you with the effect weather can have on the attenuation of light levels recorded and the associated errors in location that can result. If you know that your study species will experience different habitats at different times of the year resulting in a significantly different amount of foliage shading then different thresholds can be used during post processing to analyse different portions of data. The more you know about the bird s habitat, the more you can get out of the geolocator results. Some users choose to calibrate geolocators at different expected locations on the flight path. This has merit because local weather conditions are calibrated for that particular location, along with any temperature effects. The final data can be split into sections and the different calibration values applied accordingly.

5 Deployment After you have started the geolocators and recorded the calibration data, you are then ready to attach them to your animals. For wider discussion on attachment techniques please see the main Manual and discuss with other researchers who have attached geolocators before. It is your responsibility to abide by the laws regarding capturing and tagging animals so please ensure they are investigated and followed. It is essential that you identify where the light sensor is, and ensure it is not covered when attached to the animal. Otherwise the data will be useless. The photos below show the position of the light sensor on a range of M-Series tags. The sensor is he same on all tags, only it s position varies, so even if the geolocator you have is not one of those pictured here, you can easily find the sensor by noting what it looks like. light sensor For each study, make a summary spreadsheet for the following: Geolocator serial number Start of logging date & time (to be sure, write down local and GMT time & date) Pre-deployment calibration location: (lat & lon, if performed) Beginning of pre-deployment calibration date & time End of pre-deployment calibration date & time (this is not stopping the geolocator but is the removal of the geolocator from the calibration location, if applicable) Deployment date & time

6 Recovery date (unnecessary but important for study report) Download date & time (unnecessary but may be useful to corroborate download data) Post deployment calibration location: (lat & lon, if performed) Beginning of post deployment calibration date & time (if performed) End of post deployment calibration date & time (if performed) Notes (e.g. unusual appearance of geolocator after deployment check for obscurity above light sensor and for visual signs of damage/wear) The most important items are in bold. Use an accurate clock such as a GPS receiver; it is unwise to use your PC clock as this is often inaccurate. We strongly advise that you use Greenwich Mean Time (GMT, Zulu, Z) in all of your work to avoid confusion. If recording GMT time by taking or adding hours from the local time zone value, be sure to take into consideration the crossing of the date line when recording the date; to be sure, we advise you to record both local (L) and GMT (Z) time and date for recording start. Note that if you stop logging at any time before deployment for whatever reason, then you must update your time and date record when you restart the logging for deployment. Save these records, they will be needed to interpret the data.

7 Download Data should be downloaded from tags as soon as possible after retrieval, even before a Post-Calibration. Follow the communication instructions above. When you are asked if you want to download (RECEIVE THE DATA) start capturing the text from the terminal emulator : CAPTURE IS ON button turns from red to green. Click on [press y ] Date and time must be in the same format as seen in the screenshot above. If you make a mistake and need to press the backspace key, you can do so but you will need to edit the.txt file after the capture session as the backspace key will not have the effect you desire. The backspace key press is actually saved as a character in the.txt file and does not delete the previous character typed. However, it is easy to

8 edit the.txt file using Notepad or some other text editor after you have finished capturing all the data to make the date and time format as it should be. Downloading can tens of minutes per year of data. Ensure the connections are not disturbed during this time (i.e. don t touch the tag or wires). Observe any glitches that may upset the file and, if they happen, try downloading again until you have a clean download. When the data have finished downloading, you will be asked to enter a line of text. This is simply for you to add notes to the data if desired; no entry other than pressing Enter is necessary. You will then be asked if you want to STOP COLLECTING DATA Do NOT put the tag into SLEEP mode until you have checked the data using the Decompressor software (see Main Manual), because otherwise you may lose all your data. No data can be downloaded in SLEEP mode, and all previous data will be lost. Once you have checked the data, and if you are intending to re-deploy the geolocator after several months, you can then re-connect the geolocator, click [press n ] to download the data and follow the on-screen instructions to put the geolocator to SLEEP and conserve the battery. If you are not intending to redeploy geolocators, there is no reason to send the geolocator to sleep, and therefore data can simply be retained in the geolocator memory as a back-up (until the battery eventually fails).

9 Consider whether you want to do a post deployment calibration or not. If you find the light sensor has become opaque or obscured then we would recommend it (see Calibration section above). Please note that during download, the internal clock continues but data are not recorded. The geolocator does not save records when it is busy downloading. Thus, during download time, the geolocator may miss a record. If the geolocator is downloaded and then downloaded again, you may see one or more missing data points in the second downloaded file, corresponding to the time of the first downloading. This will be highlighted as a missing sample error message by Decompressor. This will invalidate the two days worth of data at this time and be marked SUSPECT ; essentially the data after this missing sample, but before the next two day boundary marker, will have an advanced timestamp relating to the number of sample periods missing.

10 Appendix 1 - Linux and Mac OS Instructions for Mac and Linux use are largely as above whereby a terminal emulator program is used to communicate with the interface box. The differences lie in the actual software to use. Interface box USB drivers for most operating systems can be downloaded from Zterm is a suitable terminal emulator and, for the Mac, can be found here: A baud rate of 9600 needs to be chosen (see above). Our thanks go to Kent McFarland for these notes. Appendix 2 reasons for poor connection You have connected the geolocator around the wrong way (this will not damage the device; simply swap the clips and try again). There is some transparent encapsulant (left over from manufacture), biofouling or other deposit on the pins of the geolocator clean/wipe/scratch this off and try again. The device is dead return it to us for possible data retrieval. The interface box is dead return it to us for replacement.