CytoMAP

Multidimensional Analysis Pipeline for Histocytometry (CytoMAP) https://gitlab.com/gernerlab/cytomap

https://gitlab.com/gernerlab/cytomap

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Cite As

Stoltzfus, Caleb R., et al. “CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues.” Cell Reports, vol. 31, no. 3, Elsevier BV, Apr. 2020, p. 107523, doi:10.1016/j.celrep.2020.107523.

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General Information

MATLAB Release Compatibility

  • Compatible with any release

Platform Compatibility

  • Windows
  • macOS
  • Linux
Version Published Release Notes Action
1.4.22

See release notes for this release on GitHub: https://github.com/DrStoltzfus/CytoMAP/releases/tag/1.4.22

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1.4.21

> added option to change overlap threshold in interaction plots
> made the fit plots in density model smoother and added overlay of fit functions
> added a try statement to load .wsp to deal with derived parameter names

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1.4.20

> Fixed a bug in plotting neighborhoods
> Fixed calculate distance to regions so it works for CCN
> Updated logo
> Added Highlight Neighborhoods feature in figures
> Added Model Density extension

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1.4.18

> Improved loading table of cells stability
> Fixed bug in getting names of channels for neighborhoods
> Fixed bug in generation of random points for data containing strings
> Fixed bug in gating on cell types with multiple samples

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1.4.17

> Added the option to have a beep played when a function finishes
> Stability fixes for compatibility with MATLAB 2021a
> Added *make new sample from phenotype* function to phenotype table

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1.4.13

> Added DBSCAN to clustering options
> Fixed indexing error in regions statistics of single sample
> Updated clustering window name to include data type and model name

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1.4.12

> Fixed color limits in neighborhood clustering output plots
> Tweaked how annotate regions auto-populates when switching between models
> Fixed issue where loading multiple samples broke if a phenotype had no cells

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1.4.7

> Added functionality to options button in New Figures (change point colors, invert axes etc.)
> Changed cell % cells in cluster from 0-1 to 0-100 percentages

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1.4.6

> Annotate clusters now auto-populates names when using a string based classifier channel

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1.4.4

> Increased functionality of annotate regions and annotate cells
> Moved annotation extensions to the main CytoMAP GUI

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1.4.1

fixed a bug in export csv data

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1.3.0

- Updated .wsp loader
- Added functionality to .ims overlay
- Added new dimensionality reduction tools

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To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.