File Structure Best Practices / Troubleshooting

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1 ODYSSEY v 3.0 Software Note File Structure Best Practices / Troubleshooting The following document will cover several recommendations to help streamline image and analysis retrieval within Odyssey 3.0 software. Also included are recommendations for how to organize projects so that images can be found again quickly. The last section will detail some solutions for common problems that users may experience when trying to find and open their previously scanned images. Much of this document also applies to earlier versions of the Odyssey Application software, except as noted. There are certainly many different ways to both organize and retrieve your data in this software, but for a full explanation of these options please refer to the Odyssey User s Guide: (http://biosupport.licor.com/docs/ody_user_gd_09386.pdf). I. Open an Existing Project It is usually easier to locate a scan within a project folder than it is to locate a project on a computer hard drive. This is because project folders exist within a potentially complex hierarchy of windows folders. Therefore, it is recommended that new scans are created in an already existing project, accessed via the folders view by double clicking on a project icon ( ) from the Folders View: Project folder A Windows folder which contains scans related to your work. Scan folder contains raw tiff images and other scan data Analysis folder contains a different view or analysis of the same scan The open project button in the upper left of the toolbar can also be used to open an existing project instead of using the Folders view. The Open Project command opens a Windows dialogue box which prompts you to navigate to the project folder or file that you wish to open. However, unlike navigating in the Folders View, project folders are not readily recognizable because they look exactly like an ordinary Windows folder. Therefore instead of clicking on a folder and trying to open what might not be an Odyssey project, it is easier to first find the Odyssey project file.

2 This project file is named the same as the project folder in which it is located, is the only type of file visible when using the open command, and has the.l2d file extension. (See image to the right). Note: the extension is only visible if file extensions like.doc or.jpg are visible. Select this project file and click Open. Recently used projects quick links A third quick method to open a previously used project folder is to choose a project from the most recently used project list. This list appears at the bottom of the File menu, as shown on the right: Note: Projects in the File menu that are shown in grey are not accessible because they have been moved (and the shortcut has changed location). When the Odyssey software is first installed, it defaults to show only the 4 most recently opened projects at the bottom of the File menu. The list can be increased to 10 projects by changing the Recently Used Size: option in the Application Settings menu (see below). Opening Application Settings To change recently used size to 10

3 II. Creating New Projects New projects must eventually be created, either to help you organize scans that logically fall into different research projects, or because existing projects become cumbersome because of their size. The new project button ( ) will open the New Project dialogue box: The Windows pathway shown in the Path bar may reflect the location in which the previous user of the Odyssey software saved their project, and this might not be an ideal place in which to save your own projects. Thus it is highly recommended to use the browse button (1. on left) in order to choose a location which will be easy for you to find again. Then, navigate to find a Windows folder where your other projects are located (2., below), type in a new project name (3), and click Save (4). Hint: It will generally be easier to find your projects again if you do not create new projects within an already existing project. Such a nested project organization will usually add to the confusion regarding which folders are project folders and which are scan folders within the project folder. The image Nested Odyssey projects on the next page shows a project Klaus blots which contains a nested project IFP in cells which also contains a nested project Konofagou. It will be easier to find your projects again if they are instead organized within a single Windows folder without nesting projects within one another (see example of non-nested projects on next page).

4 Nested Odyssey projects (not recommended) Four non-nested Odyssey projects within a single Windows folder. III. Streamlining file organization with personalized Application Settings The Odyssey software by design will remember the locations where the software user has saved previous projects, scans, and reports. On computers with only a single user this works fine, but in many cases there are many users who scan their samples using the same computer. This can lead to confusion because if default locations are accepted by the current user, files may end up being saved in a difficult to find location. In these situations it is recommended that each software user create their own personalized Application Settings that can be chosen when the software is opened. When first installed, the Odyssey software will show a Set Active Application Settings dialogue window (see image on right) where each user can create their own personalized settings and save locations. To create your own settings simply click Add and give your settings a name (perhaps your own name). Then, when you open the Odyssey software next, click on your Settings and hit OK to open the software using the these Settings. Hint: if the Set Active Application Settings window does not appear when the software is opened, go to the Application Settings (Settings > Application from the top menus), and in the General Tab make sure the option Select Application Settings at start-up is checked (see right).

5 IV. Troubleshooting I still can t find my project / scan! If hunting and pecking through Odyssey Folders View or using the Open Project command still does not help you to find a missing project or scan, sometimes the Windows search function (from the Start menu) may be the best option. Odyssey scan files all end with the.scn file extension, and projects files all end with the extension.l2d, so entering either of these in the search line will return a list of all scans or projects on the computer. This search can be sorted by the date on which they were last modified, or by (e.g.) the name of the scan in order to find your missing files. I can find my project, but I can t open it! This may result when the project has a lock file present which prevents it from being opened. A lock file is generated for each project when it is opened in order to prevent two copies of the same project being altered by different users working on it at the same time (which can happen if the project is saved to a network drive). The lock file is deleted when the project is closed, but if a project folder is copied to a new location while the project is still open, or if the software fails to close properly, the lock file is left intact and the project will be unavailable. The lock file bears the extension.lck and is created in the project folder and bears the same name as the project folder and the project.l2d file. Thus, for a project BYU Demo, the folder named BYU Demo may contain a lock file called BYU Demo.lck in addition to the project file BYU Demo.l2d. Deleting the lock file should enable you to open the project. I can find and open my project, but the scan has disappeared! This will happen if a scan is closed before the files necessary for viewing the scan again have been saved to the project folder. If these files have not been saved, the software will always prompt you to save changes to the project folder if you are closing a scan (see right). A misconception for many new Odyssey users is that choosing yes to this prompt might result in the permanent modification of the original scan due to changes to the image brightness and contrast. However, the Odyssey software is incapable of modifying the unprocessed 16 bit images that are generated by the Odyssey scanner, and these 16 bit images are the only data that are utilized by the Odyssey software to generate quantification information. Moreover, in actuality if you choose No to this prompt, you may lose the image data needed to open these scans at all.

6 Regardless of how the scan files have gone missing, a simple option for retrieving the scans is to download the original 16 bit tiff images from the Odyssey scanner. The Odyssey has a large hard drive that will store usually several years worth of scans which can serve as an emergency backup. The Download Scan command will open a prompt for login information on Odyssey scanner, and then you will need to navigate to find the missing scan. 1. Choose Download scan from the File menu 2. Login to Odyssey 3. Select the missing scan I want to reorganize my scans into fewer project folders. If you currently have difficulty relocating older scans because these scans are distributed across many different project folders in many different locations, it may be beneficial to reorganize your scans into fewer projects. Scan folders cannot, however, be moved manually from one project folder to another through the Windows file manager. Instead the scan folder must be imported into the Project where you would like the scan located. To do this, first open the project where you would like the scan moved. Then, chose the File > Scan > Import Scan command (right): Find the scan folder, select it and click Open. This does require you to know both the location of the scan folder and the name of the scan folder.

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