alxndrkalinin

datasets

Images and other data from the JUMP Cell Painting Consortium

morphocell

pytorch_fnet

Three dimensional cross-modal image inference

alxndrkalinin.github.io

cucim

cytominer-eval

Common Evaluation Metrics for DataFrames

BBDM

BBDM: Image-to-image Translation with Brownian Bridge Diffusion Models

CellProfiler

An open-source application for biological image analysis

copairs

Find pairs and compute metrics between them.

cytodata.github.io

CytoData Society website

Fluorescence-Reconstruction

grit-benchmark

Benchmarking a metric used to evaluate a perturbation strength

I2SB

imagen-pytorch

Implementation of Imagen, Google's Text-to-Image Neural Network, in Pytorch

MeshNet

MeshNet: Mesh Neural Network for 3D Shape Representation (AAAI 2019)

Mitocheck-MAP-analysis

Utilizing the mean average precision (MAP) metric to assess reproducibility and perturbation effect on single-cell profiles in the MitoCheck dataset.

NDC

PyTorch implementation of Neural Dual Contouring.

PatchDDM-3D

position-effect-correction

pycytominer

cytominer python package

pytorch-3dunet

3D U-Net model for volumetric semantic segmentation written in pytorch

scib

Benchmarking analysis of data integration tools

scikit-image

Image processing in Python

SegLoss

A collection of loss functions for medical image segmentation

segmentation_models_3D

Set of models for segmentation of 3D volumes

SubdivNet

Subdivision-based Mesh Convolutional Networks.

tutorials

CellProfiler tutorial pipelines and images

VollSeg

Segmentation method able to detect membrane/nuclei-labelled cells with low signal-to-noise ratio and dense packing in 2D and 3D. Available via pip package vollseg.

volumentations

Library for 3D augmentations

voxel2mesh

Voxel2Mesh: 3D Mesh Model Generation from Volumetric Data