Troubleshooting | Inscopix

Inscopix Data Processing Troubleshooting Guide: <table> <thead> <tr><th> <h6>Category</h6> </th><th> <h6>Issue</h6> </th><th> <h6>Potential Cause</h6> </th><th> <h6>Action</h6> </th></tr> </thead> <tbody> <tr> <td>Behavioral movie</td> <td>Failed to import behavioral movie</td> <td>Encoding format of the behavioral movie is not supported</td> <td> Use FFMPEG to convert video (refer to User manual) Use a different camera or software platform to record behavioral videos in supported formats (refer to User manual) </td> </tr> <tr> <td>Behavioral movie</td> <td>Visualization of the behavioral movie is slow/saccadic</td> <td>Encoding format of the behavioral movie is not supported</td> <td> Use FFMPEG to convert video (refer to User manual) Use a different camera or software platform to record behavioral videos in supported formats (refer to User manual) </td> </tr> <tr> <td>Compatibility with Mosaic</td> <td>I can't open data processed with Mosaic</td> <td> Inscopix Data Processing Software is C++ based and cannot open .mat files generated by Mosaic software. </td> <td>The tif format (import and export) is supported both by Mosaic and Inscopix Data Processing Software. Mosaic movies can be exported to tif and imported in Inscopix Data Processing Software.</td> </tr> <tr> <td>Export compressed videos</td> <td>I would like to export more than a single movie dataset as a compressed movie (to show the contours on top of my movie or export multiple panels together)</td> <td> Inscopix Data Processing Software enables the compressed video export of one video dataset at a time and cannot add the contours on top of the movie. </td> <td> You can accomplish this by using a screen recorder tool, such as (for Windows): <ul> <li>Powerpoint (2016 or later)</li> <li>Monosnap (free)</li> <li>Camtasia Studio</li> </ul> </td> </tr> <tr> <td>Export traces</td> <td>My traces contain large gaps between movies</td> <td> This is the result of non-continuous movies being added to time series. </td> <td> If this is a problem for you or in your analysis, please contact <a href="mailto:support@inscopix.com">support@inscopix.com</a> for assistance. </td> </tr> <tr> <td>General</td> <td>Failed to write</td> <td> Not enough space in disk User does not have the right to write in the project directory </td> <td>When starting an analysis session, be sure to select a new project in a directory with sufficient space. Also confirm you have permission to write to the project directory before processing data.</td> </tr> <tr> <td>Import</td> <td> Can't import Example error message: "The data file could not be opened. The file does not contain any HDF5 files to load." </td> <td> Some files listed in the xml cannot be located Files listed in the xml are only compressed RAW files that need to be decompressed to TIF or HDF5 format </td> <td> Compare recordings listed in your xml file to the recordings you are trying to open. If any files are missing, locate these files and move them to the same directory as your xml file. If your xml only lists recordings in RAW format use the Inscopix Image Decompressor to generate TIF or HDF5 format files. These can be read into the Inscopix Data Processing Software via the updated xml generated during decompression. </td> </tr> <tr> <td>Import</td> <td>The timing information of my Inscopix video is wrong</td> <td> The timing information (frame rate or "step") can be inferred when importing xml or hdf5 formats. When importing tif files, the software assumes a default frame rate of 20 Hz. </td> <td> To ensure the timing information is correct it is best practice to import files using xml or hdf5 file formats. Using the xml format is optimal as it imports all metadata and imaging data in one step. </td> </tr> <tr> <td>License activation</td> <td> License activation failed with one of the following messages: "Failed to generate binary capability request. Device not present." "Failed to send binary message. Generic communications error. General data transfer failure. Couldn't resolve host name." </td> <td> The computer needs to have some network device enabled to allow activation of the software. This is also true in the case of offline activation where there is no internet connection available. </td> <td> Enable at least one network connection, such as a wireless port. in Windows: Use a keyboard shortcut or Control Panel\Network and Internet\Network Connections Email <a href="mailto:support@inscopix.com">support@inscopix.com</a> for further assistance with license activation. </td> </tr> <tr> <td>Missing files</td> <td>Missing files when opening project</td> <td> Inscopix Data Processing software does not save data (Inscopix movies, behavioral movies, datasets imported in project) locally in the project data folder. Rather, they are saved using path to their location. If the project has been moved to a new location or a different computer, the path to the original data is no longer valid. </td> <td> Locate files using the locate file option (right click on the missing dataset in the Project). Optional: copy the original data in the Project folder before importing them when starting a new project. </td> </tr> <tr> <td>Missing files</td> <td>Missing files when opening project</td> <td>Datasets been deleted from the Project data folder</td> <td> Locate files using the locate file option (right click on the missing dataset in the Project). Optional: copy the original data in the Project folder before importing them when starting a new project. </td> </tr> <tr> <td>Motion correction</td> <td>Motion correction is not working</td> <td> Motion can appear in data for several reasons. Common reasons include changes in the field of view including shifts or rotations as well as motion resulting from the tissue being imaged. </td> <td> Improving the choice of landmark for motion correction (ensuring the landmark is not the lens border, artifact on the lens or in the movie) can improve motion correction results. Improving the reference frame (with fewer active cells) or reference region (larger region or polygon) can also improve motion correction results. Reach out to your FSC or <a href="mailto:support@inscopix.com">support@inscopix.com</a> for further assistance.</td> </tr> <tr> <td>Open Software</td> <td>Inscopix Data Processing Software does not run when I open the software</td> <td>You may not have sufficient permissions to run the software or may need to clean out the AppData folder.</td> <td> Right click on the software shortcut and select "Run as administrator." Log in using an administrator username and password. If running as an admin does not work, it’s possible that clearing out some associated files could do the trick. First, you’re going to want to find this directory, note that whatever your username is will be where “USERNAME” appears: <ul> <li>C:\Users\USERNAME\AppData\Roaming\Inscopix Data Processing\.</li> </ul> Note that location is a hidden folder, so it’s not possible to navigate to that location by clicking through the directory. Locate the “Inscopix_Data_Processing_Recent_Files” folder in that directory and move it to a different directory (like your desktop). Try starting the software again. Contact <a href="mailto:support@inscopix.com">support@inscopix.com</a> for further assistance. </td> </tr> <tr> <td>PCA/ICA</td> <td>Results appear to be missing cells</td> <td>Number of ICs in PCA/ICA settings is too small</td> <td>Increase number of ICs and run PCA/ICA again.</td> </tr> <tr> <td>PCA/ICA</td> <td>Results show cells that are over-segmented (ie: multiple ICs for one cell)</td> <td>Number of ICs in PCA/ICA settings is too high</td> <td>Decrease number of ICs and run PCA/ICA again.</td> </tr> <tr> <td>PCA/ICA</td> <td>I am not satisfied with the cell segmentation</td> <td> Out of focus cells or excess motion in your Inscopix imaging movie can result in poor performance of the PCA/ICA algorithm. </td> <td>Reach out to your FSC or <a href="mailto:support@inscopix.com">support@inscopix.com</a> for further assistance.</td> </tr> <tr> <td>Series</td> <td>I can't create a series and see the following error message: "Datasets are overlapping in time."</td> <td> The start date and time of Inscopix movies are only known by the software when importing xml or hdf5 files. This information is lost when importing tif files. The timing information of datasets can be verified by checking their metadata (right click on the dataset in the Project). </td> <td> Import Inscopix movies using xml or hdf5 files. Create series with datasets that are not overlapping in time. </td> </tr> <tr> <td>Series</td> <td>I want to concatenate my movies, but cannot find that option.</td> <td>Inscopix Data Processing Software does not include concatenation. Instead, please leverage the Series functionality.</td> <td>Use the Series concept (refer to User manual)</td> </tr> <tr> <td>Synchronization</td> <td>Datasets are not overlapping in time</td> <td>The timing information provided at import of your behavioral movie does not match the timing information from your imaging recording.</td> <td> Check the start time of your behavioral movie in experimental notes or files. Also check the start time of your imaging recording in Metadata (right click on the dataset in the Project) Reimport the behavioral movie with the desired start time based on the correc timing information or delete the behavioral movie from the project. </td> </tr> </tbody> </table> <h3></h3>

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