LBM-CaImAn-MATLAB Documentation

Currently, inputs to this pipeline are limited to ScanImage .tiff files.

Note

Only the first step of this pipeline which converts the multi-ROI .tiff into a .h5 files separate volumetric time-series requires scanimage .tiff files.

Pipeline Overview

There are 4 core steps in this pipeline:

1. convertScanImageTiffToVolume()

2. motionCorrectPlane()

3. segmentPlane()

4. collatePlanes()

Note

The core functions used to initiate this pipeline are camelCase (lowerUpperCase). Every non-core (helper/utility) function you may use, such as play_movie(), is snake_case.

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For up-to-date pipeline requirements and algorithms, see the github repository readme.

Documentation Contents

• First Steps
  • 0.1. Project Setup
    • Installation
    • Dependencies
    • Directory Structure
  • 0.2. Pipeline Usage
    • Core Parameters
    • Logging
• User Guide
  • 1. Assembly
    • 1.1. Overview
    • 1.2. Inputs
    • 1.3. Outputs
    • 1.4. Validate Outputs
  • 2. Registration
    • 2.1. Overview
    • 2.2. Inputs
    • 2.3. Rigid Registration
    • 2.4. Non-rigid Registration
    • 2.5. Outputs
    • 2.6. Validate Outputs
  • 3. Segmentation
    • 3.1. Segmentation Overview
    • 3.2. Inputs
    • 3.3. Tuning CNMF
    • 3.4. Segmentation Outputs
  • 4. Axial Collation and Correction
    • 4.1. Inputs
    • 4.2. Outputs
  • 5. Tips and Tricks
    • 5.1. Exploring Datasets in MATLAB
    • 5.2. Fullfile
    • 5.3. Learn about Functions
    • 5.4. Parallel Processing
    • 5.5. Find MATLAB Install Location
  • 6. Troubleshooting
    • 6.1. Memory
    • 6.2. Missing Compiled Binary (Windows)
    • 6.3. Matlab Server Issues
    • 6.4. Windows Filepaths
• Tutorials
  • 1. Explained: Registration
    • 1.1. Types of Registration
  • 2. Explained: Source Extraction
    • 2.1. Constrained Non-Negative Matrix Factorization (CNMF)
    • 2.2. Deconvolution
    • 2.3. Validating Neurons and Traces
  • 3. Explained: Axial Offset Correction
    • 3.1. Background
• API
  • 1. Core Functions
  • 2. Utility Functions
    • 2.1. Readers
    • 2.2. Writers
    • 2.3. Visualization
    • 2.4. Validation
  • 3. Internal Functions
• Image Gallery
  • Pre-Processing / Extraction
• Glossary
• Links