Projects

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Kidney Tissue Characterization Using Normalized Raman Imaging (NoRI) and Segment Anything

Project Lead: Ranit Karmakar

Collaborator: Kirschner Lab

AI Machine Learning Image Analysis
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Bio-Image Analysis on O2 (DIOS & ViTO)

Project Lead: Ranit Karmakar

Funded by: CCB & Dean's Innovation Award

O2 Image Analysis Software HPC
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pymmcore-plus: A Pure Python Ecosystem for Microscope Control with Micro-Manager

Contributor: Federico Gasparoli

Collaborator: Open Source

Microscopy Open-source micro-manager Python
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Quantifying Inflammation in Histopathology Slices of the Mouse Pancreas

Project Lead: Maria Theiss

Collaborator: Silver Lab

Pancreas QuPath Deep Learning
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An Image Analysis Pipeline to Quantify the Spatial Distribution of Cell Markers in Stroma-rich Tumors

Project Lead: Antoine Ruzette

Collaborator: Muranen Lab

Stroma QuPath Python StarDist
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Large Synthetic Datasets to Train Foundation Models for Cell Segmentation

Project Lead: Antoine Ruzette

Funded by: Core for Computational Biomedicine

Synthetic Dataset Generation Python
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Automated Classification of Cell Cycle Stages of FUCCI Cells Using Time-Lapse Imaging

Project Lead: Ranit Karmakar

Collaborator: King Lab

FUCCI Time Lapse TrackMate
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Developing Deep Learning Models and a Visual-Age Score for Quantifying Cellular Aging and Rejuvenation

Project Lead: Ranit Karmakar

Collaborator: Sinclair Lab

High Content Screening Cellular Aging Deep Learning
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Defeating Antibiotic Resistance through Transformative Solutions (DARTS)

Project Lead: Simon Nørrelykke

Collaborator: Paulsson Lab

Mother Machine Trenches Bacteria