Projects in Awesome Lists by marrlab
A curated list of projects in awesome lists by marrlab .
https://github.com/marrlab/basic
A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images
Last synced: 19 Apr 2025
https://github.com/marrlab/domainlab
modular domain generalization: https://pypi.org/project/domainlab/
domain-generalization-causality-deep-learning
Last synced: 15 Mar 2026
https://github.com/marrlab/instantdl
InstantDL: An easy and convenient deep learning pipeline for image segmentation and classification
classification deep-learning docker gpu image-segmentation instance-segmentation pixel-wise-regression regression semantic-segmentation
Last synced: 20 Mar 2025
https://github.com/marrlab/HistoGPT
A vision language model for gigapixel whole slide images in histopathology
Last synced: 06 May 2025
https://github.com/marrlab/shapr_torch
SHAPR: Code for "Capturing Shape Information with Multi-Scale Topological Loss Terms for 3D Reconstruction"
cubical-complexes deep-learning image-reconstruction persistent-homology pytorch segmentation topological-data-analysis topological-machine-learning
Last synced: 11 Jul 2025
https://github.com/marrlab/histogpt
A vision language model for gigapixel whole slide images in histopathology
Last synced: 19 Apr 2025
https://github.com/marrlab/dispr
A Diffusion Model Predicts 3D Shapes from 2D Microscopy Images
Last synced: 19 Apr 2025
https://github.com/marrlab/hematofateprediction
Code accompanying "Prospective identification of hematopoietic lineage choice by deep learning", Nature methods 2017, DOI:10.1038/nmeth.4182
Last synced: 19 Apr 2025
https://github.com/marrlab/dinobloom
Blood Cell Foundation Model based on DINOv2
Last synced: 19 Apr 2025
https://github.com/marrlab/med-al-ssl
Repository for implementation of active learning and semi-supervised learning algorithms and applying them to medical imaging datasets
active-learning deep-learning medical-imaging semi-supervised-learning weakly-supervised-learning
Last synced: 19 Apr 2025
https://github.com/marrlab/car_t_targetidentification
Computational identification of targets for CAR-T cell therapy in AML
Last synced: 19 Apr 2025
https://github.com/marrlab/shapr
SHAPR - An AI approach to predict 3D cell shapes from 2D microscopic images
Last synced: 19 Apr 2025
https://github.com/marrlab/scifai
scifAI: An explainable AI python framework for the analysis of multi-channel imaging data
Last synced: 13 Mar 2026
https://github.com/marrlab/scemila
Single cell based explainable multiple instance learning algorithm (SCEMILA) for genetic acute myeloid leukemia subtype classification.
Last synced: 19 Apr 2025
https://github.com/marrlab/anomaly-aware-mil
A simple pooling method for multiple instance learning based on attention and anomaly scores of instances.
Last synced: 19 Apr 2025
https://github.com/marrlab/classificationall
Accurate classification of blood cells in a small acute lymphoblastic leukemia dataset using convolutional neural networks
Last synced: 06 Jul 2025
https://github.com/marrlab/attmil
Attention Based Multiple Instance Learning (attMIL)
Last synced: 27 Jun 2025
https://github.com/marrlab/causalspyne
Python data generation tool with unobserved confounding as testbed for causal discovery and causal abstraction
Last synced: 19 Apr 2025
https://github.com/marrlab/batchdetect
BatchDetect: a python package for detect systematic batch effects in datasets
Last synced: 05 Jul 2025
https://github.com/marrlab/neurogenesisanalysis
Pre-anaylsis, neurogenesis model implementation, parameter inference procedure, model averaging, model evaluation and prediction
Last synced: 29 Mar 2025
https://github.com/marrlab/bright2nuc
Preprint: https://www.biorxiv.org/content/10.1101/2022.08.30.505835v1.full.pdf
Last synced: 29 Mar 2025
https://github.com/marrlab/gal1repression
Modeling Gal1 repression kinetics in single budding yeast cells
Last synced: 29 Mar 2025
https://github.com/marrlab/hematopoiesismodelcomparison
comparison of different lineage hierarchy models describing hematopoiesis
Last synced: 26 Jun 2025
https://github.com/marrlab/dermai_code
Code needed to preprocess and analyse data for the dermAI project
Last synced: 29 Mar 2025
https://github.com/marrlab/recap-friday
In this repository we maintain the material for recap fridays at marr lab
Last synced: 29 Mar 2025
https://github.com/marrlab/hematopoieticdisorderanalysis
Data visualization, model implementation, parameter inference and model selection for mechanistic models of hematopoiesis
Last synced: 29 Mar 2025
https://github.com/marrlab/spatiotemporalanalyses
Scripts for the paper: Emergence of aggregated spatiotemporal division patterns from redividing neural stem cells
Last synced: 29 Mar 2025
https://github.com/marrlab/classifier_calibration
Evaluation and improvement of the calibration of a classifier with temperature scaling.
Last synced: 29 Mar 2025
https://github.com/marrlab/movementanalysis
Scripts to recreate movement analysis figures
Last synced: 29 Mar 2025
https://github.com/marrlab/caitomorph
cAItomorph: Hematological Diagnostics from Peripheral Blood Cytomorphology
Last synced: 07 Jan 2026
https://github.com/marrlab/histonesxenopus
H4K20 methylation dynamics during Xenopus embryogenesis
Last synced: 07 Oct 2025
https://github.com/marrlab/vlm_cytomorphology_eval
Evaluation of large vision language models on cytomorphology tasks
Last synced: 23 Jun 2026