Processes Calcium Imaging Data
Read in the manual classifications of neurons from SCALPEL.
Read in results from SCALPEL.
Read in results from Step 0 of SCALPEL.
Read in results from Step 1 of SCALPEL.
Read in results from Step 2 of SCALPEL.
Read in results from Step 3 of SCALPEL.
Read in Y matrix for SCALPEL.
Plot the most active frames for a given neuron.
Plot preliminary dictionary element from Step 1 of SCALPEL and its cor...
Plot a summary of a given cluster from Step 2 of SCALPEL.
Plot a frame of the video.
Plot both the spatial and temporal components from Step 3 of SCALPEL.
Plot both the spatial and temporal components for the sequence of lamb...
Plot spatial components from Steps 2 or 3 of SCALPEL.
Plot temporal components from Step 3 of SCALPEL.
Plot a frame of the video with shading.
Plot a summary of the fluorescence in the video.
Manually classify the identified neurons from SCALPEL.
Manually classify the identified neurons from SCALPEL.
Save additional frames for manually classifying the identified neurons...
Save additional frames for overlapping neurons from SCALPEL.
scalpel: A package for processing calcium imaging data.
Perform entire SCALPEL pipeline.
Perform Step 0 of SCALPEL.
Perform Step 1 of SCALPEL.
Perform Step 2 of SCALPEL.
Perform Step 3 of SCALPEL.
Summarize results from SCALPEL pipeline.
Update the classifications of neurons from SCALPEL.
Update the classifications of specified neurons from SCALPEL.
Review and update the chosen threshold for image segmentation in Step ...
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>.