pgrosjean

pgrosjean.github.io

pyguide

wsi_ssl

This is a simple repository containing a single training script for fine-tuning DINO V2 with the DINO V1 loss for whole slide images in histopathology.

bmi_206_individual

This is the repository for my individual portion of the UCSF BMI 206 Project. This project focuses on chemotype enrichment and spectral characterization of essential reactions in reaction-centric metabolic networks.

BMI_Bootcamp2020

cellpose

a generalist algorithm for cellular segmentation

HE2RNA_code

Train a model to predict gene expression from histology slides.

ij1-patcher

Extension points for ImageJ 1.x via runtime patching to support (limited) headless operation and ImageJ2's legacy layer

imglib2-roi

Regions of interest (ROIs) and labelings for ImgLib2

nuclei_find

This toolkit enables the detection of nuclei in low resolution images through the use of a novel computer vision workflow. Nuclei can also be clustered to given coordinates enabling the spatial quantification of cells.

Project1

Project2

Project3