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Collection of functions for processing two-photon volume images

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.ipynb_checkpoints
.ipynb_checkpoints
 
 
odorpanelResponsesDoOR
odorpanelResponsesDoOR
 
 
AlternateMinimizationPCA_AW.m
AlternateMinimizationPCA_AW.m
 
 
IHC_loadspots.m
IHC_loadspots.m
 
 
IHC_watershed.m
IHC_watershed.m
 
 
README.md
README.md
 
 
Run HDBSCAN on raw pixel fluorescence traces.ipynb
Run HDBSCAN on raw pixel fluorescence traces.ipynb
 
 
UMAP on pixel cluster assignments.ipynb
UMAP on pixel cluster assignments.ipynb
 
 
animate3dPlot.m
animate3dPlot.m
 
 
assignGlomeruli.m
assignGlomeruli.m
 
 
assignGlomeruli_v2.m
assignGlomeruli_v2.m
 
 
assignGlomeruli_v3.m
assignGlomeruli_v3.m
 
 
assignGlomeruli_v4_useManualSeeds.m
assignGlomeruli_v4_useManualSeeds.m
 
 
assignGloms.m
assignGloms.m
 
 
assignGlomsBetterRandomization.m
assignGlomsBetterRandomization.m
 
 
batchNormalizeIHCimages.m
batchNormalizeIHCimages.m
 
 
binImage.m
binImage.m
 
 
calculateConsensusClusters.m
calculateConsensusClusters.m
 
 
calculateConsensusClustersOverlap.m
calculateConsensusClustersOverlap.m
 
 
compareManualAndAutomatedClusterLabels.m
compareManualAndAutomatedClusterLabels.m
 
 
countClustersForMultipleKmeans.m
countClustersForMultipleKmeans.m
 
 
customKmeans.m
customKmeans.m
 
 
glomeruliAssignmentCostFunction.m
glomeruliAssignmentCostFunction.m
 
 
ihc_190123.m
ihc_190123.m
 
 
initializeManualClusterLabels.m
initializeManualClusterLabels.m
 
 
makeClusters.m
makeClusters.m
 
 
mattKmeans.m
mattKmeans.m
 
 
mergeLikeClusters.m
mergeLikeClusters.m
 
 
neuronPCA_3d.m
neuronPCA_3d.m
 
 
plotALResponse.m
plotALResponse.m
 
 
plotGaussian.m
plotGaussian.m
 
 
process2DImagingKmeans.m
process2DImagingKmeans.m
 
 
processMultipleKmeans.m
processMultipleKmeans.m
 
 
processVolumeImagingKmeans.m
processVolumeImagingKmeans.m
 
 
readVolumeImage.m
readVolumeImage.m
 
 
readVolumeImageSeries.m
readVolumeImageSeries.m
 
 
runAssignGloms.m
runAssignGloms.m
 
 
runVolumeImagingKmeansForEntireFolder.m
runVolumeImagingKmeansForEntireFolder.m
 
 
segmentIHCimage.m
segmentIHCimage.m
 
 
showClusters.m
showClusters.m
 
 
showIndividualKmeansResults.m
showIndividualKmeansResults.m
 
 
visualizeClusters.m
visualizeClusters.m
 
 
visualizeClustersScript.m
visualizeClustersScript.m
 
 
volumeImagingKmeans.m
volumeImagingKmeans.m
 
 

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imaging

A collection of functions for processing two-photon fluorescence volume images Overall pipeline

  1. Load images
  2. Perform PCA
  3. Run k-means to cluster pixels
  4. Prune clusters
  5. Calculate df/f for each cluster

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Collection of functions for processing two-photon volume images

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