SPARCSpy

SPARCSpy Ecosystem

  • Quickstart
    • Installation
    • SPARCSpy workflow
      • Segmentation
      • Extraction
      • Classification
      • Selection
    • A walk through the SPARCSpy Ecosystem
      • Import Required Libraries
      • Generate the Project Structure
      • Load Imaging Data
        • Method 1: loading images from file
        • Method 2: loading images from numpy array
        • Looking at the loaded images
      • Generating a Segmentation
        • Looking at Segmentation Results
      • Extracting single-cell images
        • Look at extracted single-cell images
      • Classification of extracted single-cells
        • looking at the generated results
      • Exporting Cutting countours for excision on the LMD7
  • SPARCSpy Workflow
    • SPARCSpy Projects
      • Project classes
        • 1. Project
        • 2. TimecourseProject
      • Initializing a SPARCSpy Project
      • Loading Images into a SPARCSpy project
    • Config Files
    • Segmentation
      • Segmentation classes
        • 1. Segmentation
        • 2. ShardedSegmentation
        • 3. TimecourseSegmentation
        • 4. MultithreadedSegmentation
      • Segmentation Workflows
        • WGA segmentation
        • DAPI segmentation
        • Cytosol Cellpose segmentation
        • DAPI Cellpose segmentation
    • Extraction
      • Extraction classes
      • Single-cell image datasets
    • Classification
    • Selection
  • Example Notebooks
    • Basic SPARCSpy Project
      • A walk through the SPARCSpy Ecosystem
        • Import Required Libraries
        • Generate the Project Structure
        • Load Imaging Data
        • Generating a Segmentation
        • Extracting single-cell images
        • Classification of extracted single-cells
        • Exporting Cutting countours for excision on the LMD7
    • Timecourse SPARCSpy Project
      • Example Notebook Running SPARCSpy on datasets with multiple images
        • Some Helper Functions for visualization of results
        • Initialize a Project
        • Input Data Format
        • Example Load data using the from files function
        • Example loading data via a numpy array
        • Segmentation
        • Single-Cell Extraction
    • Segmentation Workflows
      • Example Notebook showcasing the different segmentation workflows
        • WGA Segmentation
        • DAPI Segmentation
        • Cytosol Segmentation Cellpose
        • DAPI Segmentation Cellpose

Module API

  • Command Line Tools
    • sparcs-split
      • Positional Arguments
      • Named Arguments
      • Examples
    • sparcs-stat
      • Positional Arguments
      • Named Arguments
      • Examples
    • sparcs-cleanup
      • Positional Arguments
      • Named Arguments
      • Examples
  • Module Documentation
    • processing
      • utils
      • preprocessing
      • segmentation
    • pipeline
      • base
        • Logable
        • ProcessingStep
      • project
        • Project
        • TimecourseProject
      • segmentation
        • Segmentation
        • ShardedSegmentation
        • TimecourseSegmentation
        • MultithreadedTimecourseSegmentation
      • workflows
      • extraction
        • HDF5CellExtraction
        • TimecourseHDF5CellExtraction
      • classification
        • MLClusterClassifier
        • CellFeaturizer
      • selection
        • LMDSelection
    • ml
      • datasets
      • metrics
      • models
      • plmodels
      • pretrained_models
      • transforms
      • utils
SPARCSpy
  • Module Documentation
  • View page source

Module Documentation

  • processing
    • utils
    • preprocessing
    • segmentation
  • pipeline
    • base
      • Logable
      • ProcessingStep
    • project
      • Project
      • TimecourseProject
    • segmentation
      • Segmentation
      • ShardedSegmentation
      • TimecourseSegmentation
      • MultithreadedTimecourseSegmentation
    • workflows
    • extraction
      • HDF5CellExtraction
      • TimecourseHDF5CellExtraction
    • classification
      • MLClusterClassifier
      • CellFeaturizer
    • selection
      • LMDSelection
  • ml
    • datasets
    • metrics
    • models
    • plmodels
    • pretrained_models
    • transforms
    • utils
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© Copyright 2023 Sophia Mädler, Georg Wallmann and Niklas Schmacke.

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