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matisse's Introduction

Matisse

Getting Started with Matisse, a Matlab Toolbox for the analysis of In Situ Sequencing experiments

Description

The Matlab Analysis Toolbox for Spatially resolved transcriptomics aims to provide an easy to use tool for performing a initial analyis for spot-based technologies in the field of Spatially-resolved transcriptomics, with focus on In Situ Sequencing experiments. Currently it is design to be able to analyze both non-segmented and segmented datasets, following this structure:

Alt text

System Requirements

The toolbox requires two add-ons: Image Processing Toolbox, Paralel Computing Toolbox and Bioinformatics Toolbox. The toobox as been tested in MATLAB R2019a and R2019b using Windows.

Examples

Several examples of the use of the toolbox can be found in the folder '\Examples' . Please take as a reference MATISSE_EXAMPLE_mousebrain.mlx to start your analysis.

matisse's People

Contributors

sergiomarco25 avatar

Stargazers

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Watchers

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matisse's Issues

ROI_draw_onImage as a function is not supported

Hi all,

Thank you for publishing your Insitu processing toolbox, I think it will be extremely useful going forward!

I am working with some large datasets and I need to select ROIs to get reasonable runtimes, you guys have a built in function for this, however I cannot get this to work.

When I try to call ROI_draw_onImage it throws this error:

Execution of script ROI_draw_onImage as a function is not supported:
C:\Users\USERNAME\AppData\Roaming\MathWorks\MATLAB
Add-Ons\Collections\matisse_rev\C__\Users\sergio.salas\Downloads\Tools-master\Tools->master\Automatic_pipeline\lib\ROI_draw_onImage.m
Error in matissetest3 (line 13)
CORTEX_SPOTS=ROI_draw_onImage(SPOTS,image_selected); %{'MTOR'}

Thanks for any help

Vignette Enhancement

Hi @sergiomarco25 , thanks for your excellent work! I'd like to analyze my ISS data using Matisse. However, as I am a beginner in Matlab, could you give me some recommendations on where to start? Do you have test data? Thanks a lot!

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