MERlin

• Installation
  • Set up a virtual environment
  • Installing prerequisites
  • Installing MERlin
  • Specifying paths with a .env file
• Usage
  • Input specifications
  • Executing locally
  • Executing on a high performance cluster
• Analysis tasks
  • warp.FiducialFitWarp
  • warp.FiducialCorrelationWarp
  • preprocess.DeconvolutionPreprocess
  • optimize.Optimize
  • decode.Decode
  • filterbarcodes.FilterBarcodes
  • filterbarcodes.GenerateAdaptiveThreshold
  • filterbarcodes.AdaptiveFilterBarcodes
  • segment.SegmentCells
  • segment.AssignCellFOV
  • segment.ExportCellMetadata
  • generatemosaic.GenerateMosaic
  • sequential.SumSignal
  • sequential.ExportSumSignals
  • partition.PartitionBarcodes
  • partition.ExportPartitionedBarcodes
  • slurmreport.SlurmReport
  • plotperformance.PlotPerformance
• Contributing to MERlin
  • Opening a pull request
  • Code formatting
  • Running the tests
  • Generating documentation
• API
  • merlin.core
  • merlin.analysis
  • merlin.util
  • merlin.view

Indices and tables

• Index

• Module Index

• Search Page