Overview: module code — Inscopix Data Processing Software 1.3.0 documentation                                                                                                                                                                                                                                                                 1.3                                                                                                                                                                                        

• Installation
  • System Requirements
  • Installing Inscopix Data Processing Software
    • Windows
    • macOS
    • Linux
• Overview
  • Types of Data Sets
  • Important Concepts
    • Project
    • Series
    • Master
  • Running Algorithms
  • Temporal Information
• Graphical User Interface
  • File Menu
    • User Preferences
  • Action Toolbar
  • Player Toolbar
  • Processing Panel
  • Project Panel
    • Project Tree
    • Right-Click Menu
      • View Metadata
      • Processing History
      • Import Data Here
      • Delete
      • Rename
      • Locate Missing File(s)
      • Edit Timing Information
      • Expand
  • Visualizer Panel
    • Movie and Image Visualizer
    • Trace Visualizer
    • Multi-Pane Visualization
    • Adjusting Contrast
  • Cell Panel
• Operations and Algorithms
  • Import Data
    • Microscope Movie or Snapshot Image
    • Cell Set
    • Behavioral Movie
    • GPIO
    • Events
    • IMU
    • CSV Traces
  • Time Series
    • Settings
    • Description
  • Preprocessing
    • Settings
    • Description
      • Early Frames
  • Spatial Filter
    • Settings
    • Description
  • Motion Correction
    • Settings
    • Description
    • Global Registration Weight
  • Delta F/F
    • Settings
    • Description
  • Cell Identification
    • PCA ICA
      • Settings
      • Description
    • CNMFe
      • Installation
      • Recommended Workflow
      • Running CNMFe
      • Parameter Setting Tips
      • Algorithm Description
    • Manual ROIs
      • Settings
      • Description
    • Apply Contours
      • Settings
      • Description
  • Event Detection
    • Settings
    • Description
  • Export Options
    • Export Movie
      • Settings
      • Description
    • Export Image
      • Settings
      • Description
    • Export Cell Sets, Events, IMU, and GPIO
      • Settings
      • Description
      • Pseudocode
  • Additional Tools
    • Trim Movie
      • Settings
      • Description
    • Movie Projection
      • Settings
      • Description
    • Longitudinal Registration
      • Settings
      • Description
    • Auto Accept/Reject Cells
      • Cell Metrics
    • Multiplane Registration
      • Overview
      • Settings
• Python API
  • Setup the Python API
    • Windows
      • Visual Studio 2015
      • Git Bash
      • Pre-installation Cleanup
      • Creating the isxenv Environment
    • Linux and macOS
      • XCode on macOS
      • GCC on Linux
      • Creating the isxenv Environment
  • Examples
    • Standard Workflow
      • Reference and Source Code
    • Reading Data
      • Reference and Source Code
    • Writing Data
      • Reference and Source Code
    • Computing and Plotting Metrics
      • Reference and Source Code
    • Running CNMFe through CaImAn with the Python API
      • How to run multiple patches in parallel
      • CaImAn CNMFe Example Code
  • API Reference
• MATLAB API
  • Setup the MATLAB API
  • MATLAB and Python Differences
  • Compatibility with Mosaic
  • Examples
    • Running CNMFe through MATLAB with the MATLAB API
      • MATLAB CNMF_E Example Code
• Frequently Asked Questions
  • When I try to install the Mac version of the software, I get an error message
  • Inscopix Data Processing Software crashed before I could save my work. Is there a way to recover the data?
  • How does Inscopix Data Processing Software handle dropped frames?
  • What are the units of the movies output by Delta F/F?
  • What are the units of the traces output by PCA-ICA?
  • What are the units of the traces output by Apply Contours?
  • Inscopix Data Processing Software cannot find some datasets in my project. What should I do?
  • I can’t load my behavioral data video. What should I do?
  • I am not able to create a series of movies
  • How can I get cell location/centroid coordinates?
  • Should I use PCA-ICA or CNMFe to process my data?
  • For CNMFe, instead of downsampling to 10Hz, can I trim frames?
  • Can I run longitudinal registration on cell sets output by CNMF-E?
  • Are the events output by CNMFe calcium events or action potentials?
  • Can I run IDPS event detection on the cell sets output by CNMFe?
  • Do cellsets output by CNMF-E have metrics that can be used for sorting cells?
  • Can I run isx.cell_metrics on cell sets and events output by CNMFe?
  • What version of MATLAB CNMF_E and CaImAn CNMFe are IDPS APIs using?
• Support
  • Contact Us
  • Bug Reports
• Release Notes
  • v1.3
    • v1.3.0
  • v1.2
    • v1.2.1
    • v1.2.0
  • v1.1
    • v1.1.2
    • v1.1.1
    • v1.1.0
  • v1.0
    • v1.0.0
• License
• Acknowledgements
  • Armadillo C++ Linear Algebra Library
  • OpenCV
  • JSON for Modern C++
  • HDF5 (Hierarchical Data Format 5) Software Library and Utilities
  • LibTiff
  • Intramodal Registration Software
  • Intel MKL
  • Intel Threading Building Blocks
  • FFmpeg
  • Qt
  • NumPy
  • SciPy
  • Pandas
  • Matplotlib
  • Sphinx
  • Read the Docs Sphinx Theme
  • jQuery
  • Underscore
  • Font Awesome
  • Applicable Licenses
    • Intel Simplified Software License
    • MIT License
    • Apache License 2.0
    • GNU Lesser General Public License v2.1, dated February 1999
    • GNU Lesser General Public License v3, dated June 2007
• Bibliography

                                                                                        Inscopix Data Processing Software                                                            

          
• Docs »
              
• Overview: module code
               
•               
      

                                          All modules for which code is available

• isx.algo
• isx.cnmfe
• isx.core
• isx.examples.metrics
• isx.examples.readdata
• isx.examples.standardworkflow
• isx.examples.writedata
• isx.io
• isx.util

                                                      

        © Copyright 2019, Inscopix (Doc# MAN-MKT-002777 Rev G)       Last updated on Nov 11, 2019.    

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