Package: scalpel 1.0.3

scalpel: Processes Calcium Imaging Data

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. <doi:10.1214/18-AOAS1159>. <https://projecteuclid.org/euclid.aoas/1542078051>.

Authors:Ashley Petersen

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scalpel.pdf |scalpel.html✨
scalpel/json (API)

# Install 'scalpel' in R:
install.packages('scalpel', repos = c('https://ajpete.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.20 score 32 scripts 168 downloads 5 mentions 29 exports 20 dependencies

Last updated 4 years agofrom:5ed5b98cfd. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-win-x86_64NOTEOct 27 2024
R-4.5-linux-x86_64NOTEOct 27 2024
R-4.4-win-x86_64NOTEOct 27 2024
R-4.4-mac-x86_64NOTEOct 27 2024
R-4.4-mac-aarch64NOTEOct 27 2024
R-4.3-win-x86_64OKOct 27 2024
R-4.3-mac-x86_64OKOct 27 2024
R-4.3-mac-aarch64OKOct 27 2024

Exports:getNeuronStatusgetScalpelgetScalpelStep0getScalpelStep1getScalpelStep2getScalpelStep3getYplotBrightestplotCandidateFrameplotClusterplotFrameplotResultsplotResultsAllLambdaplotSpatialplotTemporalplotThresholdedFrameplotVideoVariancereviewNeuronsreviewNeuronsInteractivereviewNeuronsMoreFramesreviewOverlappingNeuronsscalpelscalpelStep0scalpelStep1scalpelStep2scalpelStep3updateNeuronsupdateNeuronsInteractiveupdateThreshold

Dependencies:clicodetoolscpp11foreachgamglueigraphiteratorslatticelifecyclemagrittrMatrixpkgconfigprotoclustR.matlabR.methodsS3R.ooR.utilsrlangvctrs

Readme and manuals

Help Manual

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