# Processes Calcium Imaging Data

## Documentation for package ‘scalpel’ version 1.0.3

- DESCRIPTION file.

## Help Pages

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.