Man pages for scalpel
Processes 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... |
| 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... |
| plotResultsAllLambda | Plot both the spatial and temporal components for the... |
| 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... |
| reviewOverlappingNeurons | Save additional frames for overlapping neurons from SCALPEL. |
| scalpel | Perform entire SCALPEL pipeline. |
| scalpel-package | scalpel: A package for processing calcium imaging data. |
| 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. |
| 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... |
