Brain Alignment

A MATLAB-based software for aligning histological mouse brain images to the Allen Brain CCFv3

Documentation

Check out the docs folder for extensive documentation.

Name		Name	Last commit message	Last commit date
Latest commit History 20 Commits
docs		docs
utilities		utilities
.gitignore		.gitignore
A1_batchQuantifyDots.m		A1_batchQuantifyDots.m
A2_batchQuantifyDiffuse.m		A2_batchQuantifyDiffuse.m
A3_colocalizationAnalysis.m		A3_colocalizationAnalysis.m
LICENSE		LICENSE
P1_prepareMouseFolder.m		P1_prepareMouseFolder.m
P2_prepareMasks.m		P2_prepareMasks.m
P3_prepareXmlFiles.m		P3_prepareXmlFiles.m
P4_BuildXmlQuickNII.m		P4_BuildXmlQuickNII.m
P5_batchEditSliceMask.m		P5_batchEditSliceMask.m
P6_batchCreateDispFields.m		P6_batchCreateDispFields.m
README.md		README.md
Slice.m		Slice.m
Triangle.m		Triangle.m
allSlicesFromXml.m		allSlicesFromXml.m
batchBatchCellQuantify.m		batchBatchCellQuantify.m
binarizePV.m		binarizePV.m
binarizeWFA.m		binarizeWFA.m
cellClassifier.m		cellClassifier.m
cellCounter_PV.m		cellCounter_PV.m
cellLabeler.m		cellLabeler.m
checkChannelImage.m		checkChannelImage.m
checkCountMatch.m		checkCountMatch.m
checkRandomSlices.m		checkRandomSlices.m
createEditableMask.m		createEditableMask.m
getDisplacement.m		getDisplacement.m
maskEditor.m		maskEditor.m
rf01_generateTrainingImages.m		rf01_generateTrainingImages.m
rf02_trainRandomForestModel.m		rf02_trainRandomForestModel.m
triangulateSlice.m		triangulateSlice.m