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. |