Welcome to pysmFISH!

pysmFISH is a library for the analysis of single molecule fluorescence hybridization (smFISH).

pysmFISH include an API and a pipeline built to analyse large datasets.

Warning

the documentation is still not fully complete and changes will be made frequently

Content

• Index

• Installation
  • Requirements
  • Install using PyPI
  • Install from source
  • Install using conda

• Cluster setup
  • Introduction
  • Run the process locally
  • Run the process on a cluster

• API
  • filtering
  • counting
  • dots_calling
  • dots_coords_calculations
  • hdf5_utils
  • io
  • object_based_segmentation
  • utils
  • Stitching API
    • Global Optimization
    • hdf5preparation
    • hybregistration
    • inout
    • MicroscopeData
    • pairwisehelper
    • pairwisesingle
    • stitching
    • tilejoining

• Processing pipeline
  • Pipeline overview
    • Dataset structure
    • Pipeline scheme
  • Pipeline steps
    • Image acquisition
    • Initial processing
      • Create directories
      • Create configuration files
    • Filtering, raw counting and Stitching
    • Consolidate experiment
    • Transfer the stitched files and data
    • Register the stitched images
    • Create the stitched images for all genes
    • Dots coords processing
    • Staining segmentation
    • Counting dots in segmented regions
  • Scripts
    • Add coords to Experimental_metadata.yaml config file
    • Process standalone experiment
    • Preprocessing
    • Reference channel registration
    • Apply stitching to osmFISH channels
    • Staining segmentation
    • Dots coords correction
  • Configuration files
    • Experimental metadata
    • Filtering and raw counting
    • Staining segmentation
    • Coordinate file:

• License

• Author and citations
  • Cite pysmFISH

• Indices and Tables

Indices and Tables

• Index
• Module Index
• Search Page