Example Notebooks

Basic SPARCSpy Project

This notebook demonstrates the basic functionality of SPARCSpy. It shows you how to initialize a SPARCSpy project, load input images, segment, extract and classify the provided data and how to generate cutting instructions for excision on a leica LMD7 microscope.

• 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 contours for excision on the LMD7

Timecourse SPARCSpy Project

This notebook demonstrates how to use SPARCSpy to analyze a timecourse experiment. It shows you how to initialize a SPARCSpy project, load input images, segment, extract and classify the provided data and how to generate cutting instructions for excision on a leica LMD7 microscope.

• 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

This notebook walks you through the currently implemented segmentation workflows.

• Example Notebook showcasing the different segmentation workflows
  • WGA Segmentation
  • DAPI Segmentation
  • Cytosol Segmentation Cellpose
  • DAPI Segmentation Cellpose