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Welcome to the ifcb-analysis wiki!

Here you will find information about analysis tools for Imaging FlowCytobot (IFCB) data. These tools including image annotation, image processing, and image classification routines written in MATLAB.

Requirements:

• MATLAB
• MATLAB Image Processing Toolbox
• MATLAB Neural Network Toolbox
• MATLAB Statistics Toolbox
• MATLAB Curve Fitting Toolbox
• The DIPUM toolbox (which can be purchased here)

Plus optional but highly recommended:

• MATLAB Parallel Computing Toolbox

How to get the code:

• Get code using GitHub Desktop for Windows or Mac
• Get code using TortoiseGit for Windows
• Get code using git command-line tools for Linux or Mac

How use the code:

• IFCB workflow overview chart
• Flow chart for IFCB data processing
• Overview
• Access to test data and products
• Instructions for blob extraction
• Instructions for feature extraction
• Instructions for classifier application
• Make and evaluate a random forest classifier
• Instructions for manual annotation of images
• A few handy tools