Processes Calcium Imaging Data

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Documentation for package ‘scalpel’ version 1.0.3

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scalpel-package scalpel: A package for processing calcium imaging data.
getNeuronStatus Read in the manual classifications of neurons from SCALPEL.
getScalpel Read in results from SCALPEL.
getScalpelStep0 Read in results from Step 0 of SCALPEL.
getScalpelStep1 Read in results from Step 1 of SCALPEL.
getScalpelStep2 Read in results from Step 2 of SCALPEL.
getScalpelStep3 Read in results from Step 3 of SCALPEL.
getY Read in Y matrix for SCALPEL.
plotBrightest Plot the most active frames for a given neuron.
plotCandidateFrame Plot preliminary dictionary element from Step 1 of SCALPEL and its corresponding frame.
plotCluster Plot a summary of a given cluster from Step 2 of SCALPEL.
plotFrame Plot a frame of the video.
plotResults Plot both the spatial and temporal components from Step 3 of SCALPEL.
plotResultsAllLambda Plot both the spatial and temporal components for the sequence of lambda values from Step 3 of SCALPEL.
plotSpatial Plot spatial components from Steps 2 or 3 of SCALPEL.
plotTemporal Plot temporal components from Step 3 of SCALPEL.
plotThresholdedFrame Plot a frame of the video with shading.
plotVideoVariance Plot a summary of the fluorescence in the video.
reviewNeurons Manually classify the identified neurons from SCALPEL.
reviewNeuronsInteractive Manually classify the identified neurons from SCALPEL.
reviewNeuronsMoreFrames Save additional frames for manually classifying the identified neurons from SCALPEL.
reviewOverlappingNeurons Save additional frames for overlapping neurons from SCALPEL.
scalpel Perform entire SCALPEL pipeline.
scalpelStep0 Perform Step 0 of SCALPEL.
scalpelStep1 Perform Step 1 of SCALPEL.
scalpelStep2 Perform Step 2 of SCALPEL.
scalpelStep3 Perform Step 3 of SCALPEL.
summary Summarize results from SCALPEL pipeline.
summary.scalpel Summarize results from SCALPEL pipeline.
summary.scalpelStep0 Summarize results from SCALPEL pipeline.
summary.scalpelStep1 Summarize results from SCALPEL pipeline.
summary.scalpelStep2 Summarize results from SCALPEL pipeline.
summary.scalpelStep3 Summarize results from SCALPEL pipeline.
updateNeurons Update the classifications of neurons from SCALPEL.
updateNeuronsInteractive Update the classifications of specified neurons from SCALPEL.
updateThreshold Review and update the chosen threshold for image segmentation in Step 1 of SCALPEL.