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#

cell-biology

Here are 141 public repositories matching this topic...

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

  • UpdatedMar 17, 2025
  • Jupyter Notebook

Deep Learning Library for Single Cell Analysis

  • UpdatedAug 30, 2024
  • Python

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

  • UpdatedSep 15, 2020
  • Jupyter Notebook

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

  • UpdatedApr 1, 2024
  • Python

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

  • UpdatedJul 8, 2023
  • Jupyter Notebook
scPRINT

Count-Ception: Counting by Fully Convolutional Redundant Counting

  • UpdatedMay 23, 2019
  • Jupyter Notebook
u-track

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

  • UpdatedMar 15, 2025
  • MATLAB

Cell cycle inference in single-cell RNA-seq

  • UpdatedApr 25, 2023
  • Python

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

  • UpdatedMar 10, 2025
  • Jupyter Notebook
u-shape3D

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

  • UpdatedMar 15, 2025
  • MATLAB
u-track3D

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.

  • UpdatedMar 15, 2025
  • MATLAB

Automated Cell Toolkit

  • UpdatedDec 15, 2020
  • Python
u-unwrap3D

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

  • UpdatedNov 4, 2024
  • Jupyter Notebook

3D shape analysis using deep learning

  • UpdatedOct 19, 2023
  • Python
ELeFHAnt

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…

  • UpdatedJul 18, 2022
  • R

Explainable AI model of cell behavior

  • UpdatedApr 4, 2023
  • Python

Communitiy-based Cell Line Ontology

  • UpdatedJun 24, 2024
  • Shell

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