cell-biology

There are 129 repositories under cell-biology topic.

  • cellpose

    MouseLand/cellpose

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

    Language:Jupyter Notebook1.2k30824352

  • vanvalenlab/deepcell-tf

    Deep Learning Library for Single Cell Analysis

    Language:Python3961726391

  • oist/Usiigaci

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

    Language:Jupyter Notebook192142768

  • nadeemlab/DeepLIIF

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

    Language:Python14761655

  • Lee-Gihun/MEDIAR

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

    Language:Python12651827

  • deweylab/CellO

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

    Language:Jupyter Notebook6062511

  • ieee8023/countception

    Count-Ception: Counting by Fully Convolutional Redundant Counting

    Language:Jupyter Notebook515114
  • u-track

    DanuserLab/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

    Language:MATLAB4451321

  • AllenCellModeling/pytorch_integrated_cell

    Integrated Cell project implemented in pytorch

    Language:Python4366011

  • andreariba/DeepCycle

    Cell cycle inference in single-cell RNA-seq

    Language:Python354177

  • nadeemlab/ImPartial

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

    Language:Jupyter Notebook295143
  • u-shape3D

    DanuserLab/u-shape3D

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

    Language:MATLAB26462
  • u-track3D

    DanuserLab/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.

    Language:MATLAB24411

  • AllenCellModeling/actk

    Automated Cell Toolkit

    Language:Python239183
  • ELeFHAnt

    praneet1988/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 classifiers 1) RF 2) SVM and 3) LR

    Language:R21348

  • Sentinal4D/cellshape

    3D shape analysis using deep learning

    Language:Python20266

  • CLO-ontology/CLO

    Communitiy-based Cell Line Ontology

    Language:Shell196704

  • lowe-lab-ucl/cellx-predict

    Explainable AI model of cell behavior

    Language:Python1912410
  • u-unwrap3D

    DanuserLab/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.

    Language:Jupyter Notebook17200

  • HussainAther/biology

    genomics, biochemistry, biotechnology, cell biology, biophysics, ecology

    Language:Python13200

  • chan-labsite/PCNAdeep

    Track single cells and profile the cell cycle with PCNA fluorescence images

    Language:Python10202

  • Borda/kaggle_image-segm

    Simple tooling for instance segmentation aiming at cell biology...

    Language:Jupyter Notebook9302

  • KarrLab/wc_lang

    Language for describing whole-cell models as reaction networks

    Language:Python961433

  • KarrLab/wc_rules

    Rule-based modeling for whole-cell models.

    Language:Python9673

  • meyer-lab/tHMM

    A general Python framework for using hidden Markov models on binary trees or cell lineage trees.

    Language:Python931921

  • MichelML/ml-cellsignal

    CellSignal (rxrx.ai) - NEURIPS 2019 COMPETITION

    Language:HTML9302

  • DanuserLab/cmeAnalysis

    clathrin-mediated endocytosis analysis

    Language:MATLAB8342

  • MPWARE-TEAM/HPA2021

    HPA2021 solution (3rd place)

    Language:Jupyter Notebook8301

  • sarisabban/SinfNet

    A collection of datasets and neural networks for microorganism image classification

    Language:HTML8320

  • DanuserLab/u-inferforce

    u-inferforce (Traction Force Microscopy) is a MATLAB software that reconstructs traction forces of cells adhered on elastic gel doped with beads.

    Language:MATLAB7342

  • byu-biophysics/getting-started

    Introductory Git Repository for the Biophysics Research Group at BYU

    Language:Julia6316

  • CellMicroMechanics/Easy-to-use_TFM_package

    Easy-to-use traction force microscopy (TFM) software

    Language:MATLAB6103
  • u-probe

    DanuserLab/u-probe

    Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of the biosensor.

    Language:MATLAB6280

  • epitools/epitools

    Quantifying 2D cell shape and epithelial tissue dynamics

    Language:Python62800

  • Nelson-Gon/cytounet

    Deep Learning Based Cell Segmentation

    Language:Python62281

  • msymeonides/Migrate3D

    A Python package for analyzing XYZ positional data of moving objects over time

    Language:Python51