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).