Popular GitHub Repositories for Cell Segmenation

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

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

Single cell perturbation prediction

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

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)

Scalable Instance Segmentation using PyTorch & PyTorch Lightning.

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