Image Processing Scripts
Primarily pre- and post-processing of TIF stacks for ClearMap.
Full ClearMap repository found at: https://github.com/ChristophKirst/ClearMap
Email me at alexander.smith@mssm.edu with any questions.
Currently, my analysis pipeline looks like this:
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Optional - use clearMapStackCropping.py to detect brain edges & crop +/- 50 pixels, which may optimize atlas registration. Alternatively manually crop in ImageJ.
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clearMapWatershedParameters.py - Set the parameters for cell detection (as described in methods section).
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clearMapWatershedProcess.py - Performs resampling, alignment to atlas, cell detection, voxelization, and region segmentation.
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clearMapBatchProcessing.py script runs all steps from the process template other than cell detection (i.e. downsampling, registration, transformation, voxeliation, region counts) en masse for all animals at once. This saves a lot of time.
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clearMapAnalyzeTemplate.py - Once data is generated for each animal, this script runs the groupwise comparisons.
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clearMapAdvancedAnalysis.py - Runs clustering & correlational analyses (thank you to Laura DeNardo for providing a script that served as the original backbone of this).