CytoMAP

version 1.4.21 (4.88 MB) by Caleb Stoltzfus

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

https://gitlab.com/gernerlab/cytomap

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Updated 29 Jun 2021

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CytoMAP makes advanced data analytic techniques accessible for cell position and phenotype data. The goal is to take established analytical techniques, such as neural network based clustering algorithms, and package them in a user friendly way, allowing researchers to use them to explore complex cellular datasets.

Read about version changes on https://cstoltzfus.com/news

For descriptions of functions see https://gitlab.com/gernerlab/cytomap/-/wikis/home

If you run into bugs, or have questions about features; post a question on the Scientific Community Image Forum at: https://forum.image.sc/

Be sure to add the cytomap tag to your topic for visibility.

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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MATLAB Release Compatibility

Created with R2021a

Compatible with any release

Platform Compatibility

Windows macOS Linux

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Acknowledgements

Inspired by: fca_readfcs, PeterBeemiller/ImarisReader, Uniform Manifold Approximation and Projection (UMAP)

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Download	29 Jun 2021	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
Download	18 Mar 2021	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
Download	22 Feb 2021	1.4.19	> Added option to replace missing values with numbers instead of NaNs > Added extension to invert Y axis on all open plots > Added extension to bin data along the X axis
Download	12 Feb 2021	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
Download	27 Jan 2021	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
Download	15 Jan 2021	1.4.16	- Added extension for re-ordering samples - Fixed a broken export plot data - Group number in Cellularity plots now changes plot order - Added support for .xls, xlsx - Re-named file dropdown items - Selecting multiple x axes on import finds mean
Download	17 Dec 2020	1.4.15	> Fixed non-cylindrical neighborhood issue for samples with thickness close to neighborhood radius > Re-wrote merge samples to include non-conserved gates between samples > Fixed indexing error in volume normalized cellularity plots
Download	5 Dec 2020	1.4.14	> Added the option to name dimensionality reduction models > Fixed plot data export formatting issues > Fixed some of the window names > Made the 0 value of the red heatmap white
Download	30 Oct 2020	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
Download	16 Oct 2020	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
Download	13 Oct 2020	1.4.11	> Faster more stable cell-centered neighborhoods > Bigger progress bars > More stable plot click data tips > Annotate clusters now pulls existing names from all samples > Neighborhood % added to fold change in region statistics heatmap
Download	7 Oct 2020	1.4.10	> Plot Gates no longer fills in the points by default. (Added right click to enable) > Fixed issues with NaNs in neighborhoods > Import samples defaults to no Z for all samples > Indexing fix in combined cell heatmaps > Cluster result plots fix
Download	25 Sep 2020	1.4.9	> Fixed bugs in loading .csv files with mixed strings and numericals > Added compare phenotypes to cell heatmaps extension
Download	11 Sep 2020	1.4.8	> Added more options to the data export functionality > Fixed indexing problems in the Annotate Clusters GUI
Download	10 Sep 2020	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
Download	8 Sep 2020	1.4.6	> Annotate clusters now auto-populates names when using a string based classifier channel
Download	2 Sep 2020	1.4.5	> Load .csv now supports mixed numerical and string features > Load .wsp now warns if loading a derived parameter fails
Download	21 Aug 2020	1.4.4	> Increased functionality of annotate regions and annotate cells > Moved annotation extensions to the main CytoMAP GUI
Download	29 Jul 2020	1.4.3	> Added a select manual regions interface > Fixed indexing bugs in region statistics
Download	28 Jul 2020	1.4.2	> Added annotate regions extension > Added support for manually defined regions > Added annotate clustered cells > added stacked bar graphs in region statistics
Download	25 Jun 2020	1.4.1	fixed a bug in export csv data
Download	24 Jun 2020	1.4	Updated extensions bug fixes
Download	20 May 2020	1.3	- Updated .wsp loader - Added functionality to .ims overlay - Added new dimensionality reduction tools
Download	11 May 2020	1.2	Fixed install path issue
Download	4 May 2020	1.1

MLA	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.
APA	Stoltzfus, C. R., Filipek, J., Gern, B. H., Olin, B. E., Leal, J. M., Wu, Y., Lyons-Cohen, M. R., et al. (2020). CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues. Cell Reports, 31(3), 107523. Elsevier BV. Retrieved from https://doi.org/10.1016%2Fj.celrep.2020.107523
BibTeX	@article{Stoltzfus_2020, doi = {10.1016/j.celrep.2020.107523}, url = {https://doi.org/10.1016%2Fj.celrep.2020.107523}, year = 2020, month = {apr}, publisher = {Elsevier {BV}}, volume = {31}, number = {3}, pages = {107523}, author = {Caleb R. Stoltzfus and Jakub Filipek and Benjamin H. Gern and Brandy E. Olin and Joseph M. Leal and Yajun Wu and Miranda R. Lyons-Cohen and Jessica Y. Huang and Clarissa L. Paz-Stoltzfus and Courtney R. Plumlee and Thomas Pöschinger and Kevin B. Urdahl and Mario Perro and Michael Y. Gerner}, title = {{CytoMAP}: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues}, journal = {Cell Reports} }