marrlab/SHAPR

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Python
License
BSD 3-Clause "New...
Created about 3 years ago
Updated over 1 year ago

marrlab/SHAPR

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

BaSiC

A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images

DomainLab

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

InstantDL

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

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

DinoBloom

Blood Cell Foundation Model based on DINOv2

HistoGPT

A vision language model for gigapixel whole slide images in histopathology

Jupyter Notebook

HematoFatePrediction

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

Med-AL-SSL

Repository for implementation of active learning and semi-supervised learning algorithms and applying them to medical imaging datasets

CAR_T_TargetIdentification

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

Jupyter Notebook

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.

ClassificationALL

Accurate classification of blood cells in a small acute lymphoblastic leukemia dataset using convolutional neural networks

SCEMILA

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

causalspyne

Python data generation tool with unobserved confounding as testbed for causal discovery and causal abstraction

AE-CFE

attMIL

Attention Based Multiple Instance Learning (attMIL)

RedTell

BatchDetect

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

WBC-NCA

Jupyter Notebook

percollFFT

Gal1repression

Modeling Gal1 repression kinetics in single budding yeast cells

HematopoiesisModelComparison

comparison of different lineage hierarchy models describing hematopoiesis

Jupyter Notebook

Bright2Nuc

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

NeurogenesisAnalysis

Pre-anaylsis, neurogenesis model implementation, parameter inference procedure, model averaging, model evaluation and prediction