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New load/save cell-extraction outputs, EXTRACT support, and misc. updates
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@bahanonu bahanonu released this 21 Mar 08:03
· 123 commits to master since this release
v3.25.1
03d2cf1
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New

  • Added support for the new cell-extraction method EXTRACT (https://github.com/schnitzer-lab/EXTRACT-public) to CIAtah.
  • ciapkg.io.saveSignalExtraction - universal function to save NWB or CIAtah-style cell-extraction outputs
  • ciapkg.io.loadSignalExtraction - function to load either NWB or CIAtah-style cell-extraction outputs.
  • ciapkg.pkgName - Outputs the package name, e.g. CIAtah.

Updated:

  • calciumImagingAnalysisMainGui changed to ciatahMainGui.
  • computeManualSortSignals - If user hasn't called modelVarsFromFiles, computeManualSortSignals called the function. However, this lead to a mismatch between computeManualSortSignals fileNum and obj.fileNum, leading to mismatch between xcoords, etc. and input signals/images.
  • loadDependencies - Added EXTRACT support to list of functions to download.
  • ciapkg.pkgName - Option on whether to update package (only 0 for now). Also alert user if behind a version.
  • modelExtractSignalsFromMovie - Update saveRunTimes to handle case in which user selects multiple movies for cell extraction. Convert ndSparse outputs to single from cell-extraction algorithms (e.g. for CELLMax/EXTRACT) when saving as NWB. Updated EXTRACT support to include additional options.
  • signalSorter - User can now input just NWB path without a blank variable for inputSignals. Also added support for CIAtah mat files.
  • saveNeurodataWithoutBorders - Update to checking if only a single signal input.
  • computeCnmfeSignalExtraction_batch - extractedSignalsType, extractedSignalsEstType struct update.
  • changeFont - Add font name support.
  • Updated docs.
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