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scalpel (version 1.0.3)

Processes Calcium Imaging Data

Description

Identifies the locations of neurons, and estimates their calcium concentrations over time using the SCALPEL method proposed in Petersen, Ashley; Simon, Noah; Witten, Daniela. SCALPEL: Extracting neurons from calcium imaging data. Ann. Appl. Stat. 12 (2018), no. 4, 2430--2456. . .

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Version

Install

install.packages('scalpel')

Monthly Downloads

96

Version

1.0.3

License

GPL (>= 2)

Maintainer

Ashley Petersen

Last Published

February 3rd, 2021

Functions in scalpel (1.0.3)

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.
plotResultsAllLambda

Plot both the spatial and temporal components for the sequence of lambda values from Step 3 of SCALPEL.
getScalpelStep2

Read in results from Step 2 of SCALPEL.
getScalpelStep1

Read in results from Step 1 of SCALPEL.
updateNeurons

Update the classifications of neurons from SCALPEL.
getScalpelStep3

Read in results from Step 3 of SCALPEL.
updateNeuronsInteractive

Update the classifications of specified neurons from SCALPEL.
scalpelStep0

Perform Step 0 of SCALPEL.
plotSpatial

Plot spatial components from Steps 2 or 3 of SCALPEL.
scalpel

Perform entire SCALPEL pipeline.
reviewNeuronsMoreFrames

Save additional frames for manually classifying the identified neurons from SCALPEL.
scalpelStep3

Perform Step 3 of SCALPEL.
reviewNeuronsInteractive

Manually classify the identified neurons from SCALPEL.
plotFrame

Plot a frame of the video.
summary

Summarize results from SCALPEL pipeline.
plotThresholdedFrame

Plot a frame of the video with shading.
plotTemporal

Plot temporal components from Step 3 of SCALPEL.
updateThreshold

Review and update the chosen threshold for image segmentation in Step 1 of SCALPEL.
plotResults

Plot both the spatial and temporal components from Step 3 of SCALPEL.
getNeuronStatus

Read in the manual classifications of neurons from SCALPEL.
getScalpel

Read in results from SCALPEL.
reviewNeurons

Manually classify the identified neurons from SCALPEL.
plotVideoVariance

Plot a summary of the fluorescence in the video.
scalpelStep1

Perform Step 1 of SCALPEL.
scalpel-package

scalpel: A package for processing calcium imaging data.
reviewOverlappingNeurons

Save additional frames for overlapping neurons from SCALPEL.
scalpelStep2

Perform Step 2 of SCALPEL.
getScalpelStep0

Read in results from Step 0 of SCALPEL.