q-bio Summer School and Conference, 2022

Joshua Cook


Joshua Cook

Colorado State University

Collaborators: Luis Aguilera, Colorado State University; Linda Forero, Colorado State University; Timothy Stasevich, Colorado State University; Eric Ron, Colorado State University; Brian Munsky,Colorado State University

Title: Automated pipeline to process single-molecule Fluorescence In Situ Hybridization (smFISH) images

Short Abstract:  Mathematical modeling of cellular pathways is used widely in biology to comprehend molecular mechanisms thoroughly. These models require large amounts of experimental data to be validated correctly. Fluorescence in Situ Hybridization (FISH) is a well-established technology used to detect the transcriptional expression of any gene. Here, we work towards implementing a fully automated image processing pipeline to process FISH data by using Cellpose and BIG-FISH. The resulting code allows to correctly process hundreds of images for segmentation and spot quantification.

Link to Full Abstract: Joshua_Cook

Contact: jcook10@colostate.edu