Popular GitHub Repositories for Cell Populations

StarDist - Object Detection with Star-convex Shapes

一种基于迭代多大型语言模型的共识框架，用于提高单细胞RNA测序数据中细胞类型注释的准确性

Deep Learning Library for Single Cell Analysis

DANCE: a deep learning library and benchmark platform for single-cell analysis

? immunarch [R package] – Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Scientific Large Language Models: A Survey on Biological & Chemical Domains

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

Single cell perturbation prediction

Topological Deep Learning

Nested LSTM Cell

A python package for simulating movement and spatial cell types (e.g. place cells, grid cells) in continuous environments.

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

Message Passing Neural Networks for Simplicial and Cell Complexes

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

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

A recurrent attention module consisting of an LSTM cell which can query its own past cell states by the means of windowed multi-head attention. The formulas are derived from the BN-LSTM and the Transformer Network. The LARNN cell with attention can be easily used inside a loop on the cell state, just like any other RNN. (LARNN)

Machine learning approach of automatic identification and counting of blood cells (RBC, WBC, and Platelet) with KNN and IOU based verification.

Scalable Instance Segmentation using PyTorch & PyTorch Lightning.

HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)