Inscopix Data Processing v1.3.1

<ul> <li><a href="#Reqs">System Requirements</a></li> <li><a href="#Installer">Installer Downloads</a></li> <li><a href="#Sample%20Projects"></a><a href="#Docs">Documentation</a></li> <li><a href="#Sample%20Projects">Sample Projects with Longitudinal and Multiplane Data</a> </li> <li><a href="#Release%20Noes">Release Notes</a></li> </ul> <h3><a></a>System Requirements</h3> In order to run Inscopix Data Processing Software efficiently, your system should have access to a permanent storage device with fast read/write access and plenty of space. Below are recommended specifications for a system to run Inscopix Data Processing Software efficiently: <ul> <li>RAM: 32GB. (Important: CNMFe uses significantly more system memory than PCA-ICA. We recommend that you have at least 64GB of system memory on your machine prior to running the algorithm.)</li> <li>Hard Drive: 1TB SSD.</li> <li>Processor: Intel(R) Xeon 3.00GHz.</li> </ul> <table> <tbody> <tr> <td>Inscopix Data Processing Software currently supports 64-bit versions of the following operating systems.</td> <td>Inscopix Data Processing Software currently supports APIs for the following:</td> </tr> <tr> <td> <ul> <li>Windows: Windows 7 Professional and Windows 10 Pro</li> <li>macOS: El Capitan (10.11) and Sierra (10.12)</li> <li>Linux: CentOS 7</li> </ul> </td> <td> <ul> <li>MatlabR2017B</li> <li>Python 3.6</li> </ul> </td> </tr> </tbody> </table> <h3><a></a>Inscopix Data Processing v1.3.1 Installers:</h3> <table> <tbody> <tr> <td> Windows: Windows 7 Professional and Windows 10 Pro </td> <td> <a href="https://support.inscopix.com/inscopix/filedownloads/32056"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" />Download</a> </td> <td>Installation note: When opening an installer, you may see a message indicating the publisher cannot be verified. Select "Run" to proceed with the installation.Important: Run the Inscopix Data Processing Software installer with administrator privileges so that the software can be installed for all users.</td> </tr> <tr> <td> Mac: OSX 10.11 and OSX 10.12 </td> <td> <a href="https://support.inscopix.com/inscopix/filedownloads/32057"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" />Download</a> </td> <td>Installation note: Mount the Inscopix Data Processing Software disk image (.dmg) file by double-clicking on it. After agreeing to the end user license agreement by clicking on the Agree button, simply drag and drop the application into your Applications directory in the Finder window that appears to install the software. After that open the Applications directory by double-clicking on it, right-click on Inscopix Data Processing.app and click on Open in the menu that appears. After a short verification process, you will be asked to confirm that you want to open the application. You can do so by clicking on the Open button. From there, you should be able to open the application as normal.</td> </tr> <tr> <td> Linux: CentOS 7 </td> <td> <a href="https://support.inscopix.com/inscopix/filedownloads/32058"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" /> Download</a> </td> <td>Install the software by running sh Inscopix+Data+Processing+1.3.0.sh. You will need the sh, tar, gunzip and tail utilities.</td> </tr> </tbody> </table> <a></a>Documentation: <table> <tbody> <tr> <td> <a href="https://support.inscopix.com/inscopix-data-processing-130-user-guide-html"> </a><a href="https://support.inscopix.com/inscopix-data-processing-131-user-guide-html"><img src="image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAOEAAADhCAMAAAAJbSJIAAAAdVBMVEX///8AAAD29vaTk5O4uLjX19fb29vx8fHk5ORhYWHNzc12dnajo6MoKCidnZ1kZGSpqal6enpcXFyJiYnCwsKXl5dSUlJLS0siIiIyMjJvb2+wsLCDg4McHBxqamrs7OxFRUUVFRULCwu+vr49PT0mJiY2NjZL3GYGAAAHBUlEQVR4nO2d63qiMBCGkaPioSrU1trV2u72/i9xRXuy8yXOQBDMM+/P7UoykMwpkyQIFEVRFEVRFEVRFEVRFEVRFEVRFEVRFEVRFEVRFBFZWsazaLFdrh4qVsvtIpptyjTrumPNCZNNcfc4MPM4KjZJ2HU3a5JMtjbZzuTcTpKuuyskj/4yhfvmJcq77jaT4Xwplu6T5XzXdfcvkUbT2uKdWM+GXQthZnffVLwT77N+KtnNixPxTjzEXYvzm3ThULwTRZ+mZOny832z6otyne9bka9i2ofBet+aeCfmHcsXtSxfxaRD+WZXkK9i05F8c34Xp6txMdnEZZ4kaZLkZbyZFOMV33o+lh3Il/9j9W0UxYnZfmdJHI1eOc95Sa8oW8VudblTy1nOi4vCfDa6/LjxVYOsiwpmOZd6lwyH/XpqNbePq9fnupY6f95bn/x+naEa3ll7UTTrRVLYn+5ICBuxrQNPLvys/MnSwr7tZEBomSxrd/Nk825u5tlZK4jS3PCd25ebbI0t/WtxNo7NL9Z9qJM9G1ubOW/sxNCYOovaMVWh0Sg9tNKg0UmL2mjtA6OMLYSOJhvx3K6rEZrGquv3OvyD2xm1n2rYGd7tymkrBh26lujPMIknxWI8Hi+KSSzK5Cc4CHl1mHY0zAa+/Usn9EOMJnytb9ABb3WEQWArP+J+htych1twFUaIgw83kzFbw4czY9Ls/kL4FzGzv3ii3NWX64shfPKW9+OdzcX85Ik5n6CX87exKs9hp3gfMDT7QOcwg1v4GfcNtfkGPXTF65AkT8Xzw0KYWWjkpsJk6D3rp0M8fU2seUMVvrUG/g30J3g2cCKSr4KXFk3RT2tnxpGaYPq89jwAhqcXwwfw05qRKTJBvCxCVm8dccozHCjPUSueQnaeNxywgeHAm4wokcJTDmcgtcXTWvUF5IqIJqPYvQECMgdREwG5IqJpIBQRCPjA+2XWSMDBgOnEAX0jEhHMQaafFjQtVpgy2wE+nEDdAC3KzeHVMRPncJ1pYKzZRgPYQa6qkht6CndFFDhczIVG8HK437+ZlvmEG7sDF44VEoBXw/76Ml/UxJrbHAj9GT4liCbYArpa9Wav3AMRLw4AEA+yBQwdCTgYsMNaIOIFcwO8BX4pBDfgvcyY3SZVbXZzA8w13+Fzo2ZO8AN3qjasrgk114IlSU5OhssTv1kaalhGAPXVBC01ddfOEdRf0jdrnFjUEEoy527LoyTREPUxDWaRhl1sw1TBKoth8yppmpphOI+BGpXkInHasT6S9BI1U39Y/4vtPR1xXUK7kDRO1fiS/icacMlqyRwLOBiIWqfJYjKRqc6VZT5glq8RskQvNYu/hjl9ByNRA07CpnOEZaU0pj3TItSWPcqeD1OPzZAuK5E6ipeff6V7eKTrq84FFE5EpG1+JG7oJJTmyd2FFd9I182oPf8KFhPyJ4GzZnpEc8RFVtR9+/wL+QOyl3as9Xw1ka+3kIKRO5Po8hU596q0To0+NVnHWgZqKGqs/9urQutRo5aUev/VZCb/KPK3P3C/7Unot31AfPAR6ludQhx3CYxv+KmMb6jJKKmprlXA0RcJac59DdwZ374hTZD6Ng9B3OSbLgXj1DN7CBwS33waoIB880uB1fcstkCfwLP4EKQ5pDF+89Xt37iN8UFC37M8DZpInuXaUBc9y5ei5VTPct7InPi1bnGAbPrzbO0JvYrbWD+kC7tGFUK1jWdrwEHwRv6zZ+v4yKzwh8vOoYSt1WKgdIRf9TQBmrZ+1UQFSPX6Vdd2+BL7+iLeRG0iVPt+1ZfCfvpVIwxDIb/qvGFiya9afRgp+LXfAorI3DPTzLW52p4ZHO95te8Ji8hLo9b/ilfdu4bz2F7tP8SDwas9pIYZ5dM+4MOM2oPnMfdyW456AnS0l/swJpAvzdyPL/mMvA/Ywn78AO+W9elMhcAQuTs9F4PZx5bOxQhMca0/Z5sYH+7P+TSB0Q/z54yhALryB6aixYU+nxMVGA4B8eisrwClw0/4cl7bgZ3JnfblzL3AsgjqybmJge1wTz/OvgxMjuERP84vDazHlHtxBu2Bne2mBzfnCNsc9tbPEa6wnzZfNOtC2v1Z0Acy+9niN3+ed0Vp70l1Jru0M2mfzmSvYFRe3PS5+gcyXjrtZu9GqEj49+fc5P0WFaWbNd+LdHVHSUXMu8ejEV3fpfPm5iay3spX0dJ9VhW9uO+pIjW7yU3ozZ1dFReThnJ6de/akdJluf6qL8PznHDuZkb29f7DI7vGQvb6DssTWVxf79zAPaQfJDOcQrZxO3fJfpLOx1yn7gbvA/4ijYutzem56Tudf1Ddyz053stdXcy98ulebkVRFEVRFEVRFEVRFEVRFEVRFEVRFEVRFEVRlOvyHx7aa848TTLsAAAAAElFTkSuQmCC" alt="" width="30" height="29" /> View HTML User Guide</a> </td> <td> <a href="https://support.inscopix.com/inscopix/download/29806"></a><a href="https://support.inscopix.com/inscopix/download/32059"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" /> Download PDF User Guide</a> </td> </tr> </tbody> </table> <a></a>Sample Projects To help familiarize you with the recommended Inscopix Data Processing Software, our scientists have prepared 2 processed projects you can use to explore and understand our recommended workflow. One project demonstrates spatial filtering to longitudinal registration and the second demonstrates multiplane de-interleaving to cell identification. Project 1 - Longitudinal Data: This project is composed of data acquired in the mouse somatosensory cortex (S1), using nVista with AAV1.CaMKIIa.GCaMP6f (UPenn) and a 1mm diameter x ~4.3mm long prism probe. Full methods can be found in the following <a href="https://www.jove.com/video/55579/multi-layer-cortical-ca2-imaging-freely-moving-mice-with-prism-probes">JoVE video protocol</a> and <a href="https://www.jove.com/pdf/55579/jove-protocol-55579-multi-layer-cortical-ca2-imaging-freely-moving-mice-with-prism-probes">paper</a>. Note that Day1 and Day2 of the sample project correspond to Day1 and Day 4 in the JoVE protocol, respectively. <ul> <li>Day 1: the animal was placed in a behavioral arena devoid of any objects (Open Field)). Four 5-minutes nVista movies with 2 minutes pauses between movies were acquired. The associated behavioral movie is “Trial 29”</li> <li>Day 2: two texturally different objects (gel pad and wood block) were placed in the arena. Four 5-minutes nVista movies with 2 minutes pauses between movies were acquired. The associated behavioral movie is “Trial 33”</li> </ul> Note that for the purpose of reducing the size of the sample project, the original nVista movies have been cropped and downsampled spatially and temporally by a factor of 2, resulting in a sampling frequency of 10 Hz and spatial size of 538 x 474 pixels to produce the “preprocessed” movies shown in the sample project. <ul> <li>For nVista movies acquired on the same day, <a href="https://support.inscopix.com/sites/default/files/sphinx/2551/overview.html#series">series </a>were created to process them together. The details of individual datasets of a series can be accessed through the <a href="https://support.inscopix.com/sites/default/files/sphinx/2551/gui.html#view-metadata">View Metadata</a> option in the right click menu.</li> <li>For all the other datasets in the project, the details of the processing step and parameters used to generate each dataset can be accessed through the <a href="https://support.inscopix.com/sites/default/files/sphinx/2551/gui.html#processing-history">Processing History</a> option in the right-click menu.</li> <li>Sorting of cells was performed using both the auto-sorting feature and manual inspection.</li> </ul> <table> <tbody> <tr> <td> Sample Project 1 - Longitudinal Data Includes data from both days of recording, results from automatic cell sorting by an Inscopix data scientist, and longitudinal registration. Total size = ~58 GB compressed and ~74GB uncompressed </td> <td> <a href="https://support.inscopix.com/inscopix/filedownloads/19271"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" /> Download</a> </td> </tr> </tbody> </table> Project 2 - Multiplane Data: This project is composed of multiplane calcium data acquired at 50 Hz (~16.67 Hz per plane) in the mouse prefrontal cortex (PFC) using nVista 3.0 while the mouse was freely behaving in an open square cage. To reduce the size of this sample project, the original nVista movie was cropped, downsampled spatially by a factor of 3, and trimmed to 12 minutes long to produce the “raw” calcium movie shown in the sample project ("2019-10-07-16-08-22_video-DS-TPC.isxd"). The behavioral video ("Trial 11 SAAV_IM7.mpg") was only recorded for 12 minutes and has not been trimmed. The behavior recording was set up to send a 5V TTL signal to the nVista GPIO-1 port for the duration of the behavioral video recording for synchronization purposes (this signal can be seen in the .gpio file). The calcium video has been trimmed to that 12 minute time period, but the GPIO file has not been trimmed so that you can see the TTL signal that arrived from the behavior recording. The following processing has been done: <ul> <li>The 3-plane raw multiplane movie has been de-interleaved into 3 separate planes. The details of individual planes of the multiplane movie can be accessed through the <a href="https://support.inscopix.com/sites/default/files/sphinx/2551/gui.html#view-metadata">View Metadata</a> option in the right click menu. Each individual plane contains the efocus value within the filename in the project tree (170, 370, and 570) and each plane has further processed files that are linked to it in a tree structure.</li> <li>For all the other datasets in the project, the details of the processing step and parameters used to generate each dataset can be accessed through the <a href="https://support.inscopix.com/sites/default/files/sphinx/2551/gui.html#processing-history">Processing History</a> option in the right-click menu.</li> <li>Sorting of cells was performed for all planes using PCA-ICA and the auto accept/reject feature. PCA-ICA was performed using the delta F/F (DFF) movies, so viewing cell traces in single cell mode will display the DFF movie.</li> <li>For the middle plane (efocus 370), CNMFe was also run to sort cells and subsequently identified cells were manually accepted/rejected by an Inscopix scientist. CNMFe was performed using the motion corrected (MC) movie, so viewing cell traces in single cell mode will display the MC movie.</li> </ul> Note that there are 2 CSV files associated with the motion correction step (MC) for each plane that you won't see in the project tree in the IDPS GUI, but will see if you open the actual data folder associated with the project. These contain the crop and translation coordinates that were applied for the motion correction step. <table> <tbody> <tr> <td> Sample Project 2 - Multiplane Data Includes 3 planes of data from 12 minutes of recording and results from PCA-ICA cell sorting (all planes) and CNMFe cell sorting (middle plane only) by an Inscopix data scientist. Total size = ~37 GB compressed and ~51 GB uncompressed </td> <td> <a href="https://support.inscopix.com/inscopix/filedownloads/32644"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" /> Download</a> </td> </tr> </tbody> </table> <a></a>Release Notes: <ul> <li>Add support for running the CNMFe Python API on isxd movies with more than 65535 frames. **Note: you will need to update the <code>isxenv</code> conda environment to use this feature.</li> <li>Improved Python API installation process for Windows.</li> <li>Add exposure time to metadata for movies.</li> <li>Fix: IMU files no longer fail to display some traces.</li> <li>Fix: Multiplane movies with early frames now de-interleave properly.</li> <li>Fix: Importing corrupt files no longer crashes IDPS.</li> <li>Fix: Imported tiff files now have default spacing information that matches nVoke2/nVista3.</li> </ul>

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