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.

Segmentation Workflows#

This notebook walks you through the currently implemented segmentation workflows.

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.

Stitching Workflow#

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

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).