Inscopix Data Processing v1.2.1

<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 Project with 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 v1.2.1 Installers:</h3> <table> <tbody> <tr> <td> Windows: Windows 7 Professional and Windows 10 Pro </td> <td> <a href="https://support.inscopix.com/inscopix/filedownloads/25826"><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/25827"><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/25825"><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+1.1.0.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-121-user-guide-html"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" /> View HTML User Guide</a> </td> <td> <a href="https://support.inscopix.com/inscopix/download/25828"><img src="http://i.imgur.com/8Vh3834.png" width="30" height="30" /> Download PDF User Guide</a> </td> </tr> </tbody> </table> <a></a>Sample Project with Data: To help familiarize you with the recommended Inscopix Data Processing Software, our scientists have prepared a processed project you can use to explore and understand our recommended workflow (from spatial filtering to longitudinal registration). The 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/1989/html/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/1989/html/overview.html#right-click-menu">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/1989/html/overview.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 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> <a></a>Release Notes: <ul> <li>Export a cell set contour map with a custom background image.</li> <li>Add an option to the Preprocessing algorithm to automatically remove early frames from movies. Also add an option to the Trim Movie operation to manually perform the same behavior when the movie does not support automatic removal.</li> <li>Fix Event Detection and Cell Metrics on cell sets with dropped frames.</li> <li>Update the environment.yml file for the Python API to resolve some issues when installing on Windows.</li> <li>Update the Python API setup instructions, especially for Windows users.</li> <li>Update the MATLAB API setup instructions.</li> <li> Fix some minor bugs related to derived data sets. </li> </ul>

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