An Interactive Image Segmentation Filter for Multiplex Microscopy.

CyLinter is quality control software for identifying and removing cell segmentation instances corrupted by optical and/or image-processing artifacts in multiplex microscopy images. The tool is user-guided and comprises a set of modular and extensible QC modules instantiated in a configurable Python Class object. Module results are cached to allow for dynamic restarts.

CyLinter development is led by Greg Baker at the Laboratory of Systems Pharmacology, Harvard Medical School.

Funding: This work is supported by the following:

• NCI grant U2C-CA233262: Pre-cancer Atlases of Cutaneous and Hematologic Origin
• NIH grant U54CA225088: Systems Pharmacology of Therapeutic and Adverse Responses to Immune Checkpoint and Small Molecule Drugs
• Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation

Instructions: https://labsyspharm.github.io/cylinter/