Tutorials

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 a Leica LMD7

Segmentation Workflows

This notebook walks you through the currently implemented segmentation workflows.

• Different segmentation workflows
  • Overview of Segmentation Methods
  • Loading input images
  • Prepare for execution of scPortrait workflow
  • Segment input image with different segmentation algorithms

Deep Learning in scPortrait

This notebook walks you through creating a pyTorch dataloader from your scPortrait single-cell image dataset and how to utilize transforms to augment your data.

• Deep learning with scPortrait
  • Creating a Dataloader
  • Augmenting Images
  • Using scPortrait single-cell image datasets with existing DL libraries

Parsing Workflow

This notebook walks you through using scportrait’s parse module to prepare imaging data obtained from an Opera Phenix microscope for downstream applications.

• Automatically parse image files from Opera Phenix imaging experiments

Stitching Workflow

This notebook walks you through using scportrait’s stitch module to assemble whole-slide images from individual tif images.

• Stitch individual tif files into whole-slide images
  • Single-threaded Stitching
  • Multi-threaded Stitching
  • Visualize Stitching Output

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](MannLabs/scPortrait-notebooks).