cell-biology

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

deep-learning pytorch stitching segmentation datasets image-segmentation multiplex super-resolution immunohistochemical-images cell-segmentation digital-pathology pathology whole-slide-imaging cell-biology cloud-native-applications multitask-learning pathology-image pathology-gan immunohistochemistry ai-ready

UpdatedMar 18, 2025
Python

Lee-Gihun /MEDIAR

Star151

(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"

pytorch biomedical multi-resolution cell-segmentation instance-segmentation cell-biology pytorch-implementation multi-modality pytorch-segmentation monai vision-transformer neurips-2022 miscroscopy

UpdatedApr 1, 2024
Python

deweylab /CellO

Star65

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

machine-learning bioinformatics rna-seq computational-biology ontologies cell-type-classification single-cell-rna-seq cell-biology cell-type

UpdatedJul 8, 2023
Jupyter Notebook

cantinilab /scPRINT

Star55

single cell foundation model for Gene network inference and more

open-source embeddings rnaseq zero-shot-learning denoising single-cell-rna-seq cell-biology batch-correction gene-regulatory-network celltype-annotation large-language-models llms large-cell-models zero-imputation

UpdatedMar 18, 2025
Jupyter Notebook

ieee8023 /countception

Sponsor

Star51

Count-Ception: Counting by Fully Convolutional Redundant Counting

machine-learning computer-vision deep-learning cell-biology cell-counting

UpdatedMay 23, 2019
Jupyter Notebook

Multiple-particle tracking designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events

bioinformatics particle-tracking cell-biology particle-trajectories

UpdatedMar 15, 2025
MATLAB

AllenCellModeling /pytorch_integrated_cell

Star44

Integrated Cell project implemented in pytorch

python machine-learning pytorch generative-adversarial-network neural-networks autoencoder science-research cell-analysis cell-biology

UpdatedJul 6, 2023
Python

andreariba /DeepCycle

Star44

Cell cycle inference in single-cell RNA-seq

rna-seq deep-learning single-cell cell-biology

UpdatedApr 25, 2023
Python

nadeemlab /ImPartial

Star36

Interactive deep learning whole-cell segmentation and thresholding using partial annotations

deep-learning interactive pytorch segmentation cell-segmentation denoising instance-segmentation cell-biology

UpdatedMar 10, 2025
Jupyter Notebook

DanuserLab /u-shape3D

Star29

Detect morphological motifs, such as blebs, filopodia, and lamellipodia, from 3D images of surfaces, particularly images of cell surfaces.

matlab image-analysis cell-biology light-sheet-microcopy morphology-analysis

UpdatedMar 15, 2025
MATLAB

DanuserLab /u-track3D

Star26

Multiple particle tracking in dense 3D particle fields complemented with dynamic regions of interest and trackability inferences for the automated exploration of large volumetric sequences.

bioinformatics particle-tracking cell-biology particle-trajectories

UpdatedMar 15, 2025
MATLAB

AllenCellModeling /actk

Star24

Automated Cell Toolkit

pipeline biology image-processing microscopy cell-biology

UpdatedDec 15, 2020
Python

DanuserLab /u-unwrap3D

Star23

Transform 3D cell surfaces into different representations including topographic maps, 3D spheres, and 2D images for doing optimized quantification, data analysis and machine learning.

python image-analysis topography mesh-processing cell-biology morphology-analysis light-sheet-microscopy surface-unwrapping

UpdatedNov 4, 2024
Jupyter Notebook

Sentinal4D /cellshape

Star23

3D shape analysis using deep learning

deep-learning cell-biology geometric-deep-learning cancer-biology

UpdatedOct 19, 2023
Python

praneet1988 /ELeFHAnt

Star21

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It uses an ensemble of three machine learning classif…

machine-learning scalability classification single-cell annotation-tool harmonization ngs-analysis single-cell-rna-seq cell-biology celltype-annotation