Marr Lab

InstantDL

InstantDL: An easy and convenient deep learning pipeline for image segmentation and classification

DomainLab

modular domain generalization: https://pypi.org/project/domainlab/

SHAPR_torch

SHAPR: Code for "Capturing Shape Information with Multi-Scale Topological Loss Terms for 3D Reconstruction"

DISPR

A Diffusion Model Predicts 3D Shapes from 2D Microscopy Images

HematoFatePrediction

Code accompanying "Prospective identification of hematopoietic lineage choice by deep learning", Nature methods 2017, DOI:10.1038/nmeth.4182

SHAPR

SHAPR - An AI approach to predict 3D cell shapes from 2D microscopic images

CAR_T_TargetIdentification

Computational identification of targets for CAR-T cell therapy in AML

HistoGPT

Generating highly accurate pathology reports from gigapixel whole slide images with HistoGPT

scifAI

scifAI: An explainable AI python framework for the analysis of multi-channel imaging data

Anomaly-aware-MIL

A simple pooling method for multiple instance learning based on attention and anomaly scores of instances.

SCEMILA

Single cell based explainable multiple instance learning algorithm (SCEMILA) for genetic acute myeloid leukemia subtype classification.

AE-CFE

attMIL

Attention Based Multiple Instance Learning (attMIL)

BatchDetect

BatchDetect: a python package for detect systematic batch effects in datasets

Bright2Nuc

Preprint: https://www.biorxiv.org/content/10.1101/2022.08.30.505835v1.full.pdf

DinoBloom

Blood Cell Foundation Model based on DINOv2

Gal1repression

Modeling Gal1 repression kinetics in single budding yeast cells

percollFFT

RedTell

Recap-Friday

In this repository we maintain the material for recap fridays at marr lab

AE-CFE-1

dermAI_code

Code needed to preprocess and analyse data for the dermAI project

HematopoieticDisorderAnalysis

Data visualization, model implementation, parameter inference and model selection for mechanistic models of hematopoiesis

initial-data-point-selection

marrlab-blog

MILPLE

MLL23

A large publicly available single-cell peripheral blood dataset for domain generalized hematological disease diagnostics

patch-visualization

pxpermute

scifAI-notebooks

scifAI-notebooks: notebooks, analysis and tutorials using the scifAI python packages