Example Notebooks

Basic scPortrait Project

This notebook demonstrates the basic functionality of scPortrait. It shows you how to initialize a scPortrait 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 scPortrait 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

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

Additional Notebooks

Within scPortrait we provide a variety of different example datasets with an example processing notebooks. These notebooks are designed to give you a quick overview of the functionality of scPortrait and to help you get started with your own data. You can find all of the example datasets and there notebooks here.