cell-biology
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a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
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Mar 17, 2025 - Jupyter Notebook
Deep Learning Library for Single Cell Analysis
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Aug 30, 2024 - Python
Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning
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Sep 15, 2020 - Jupyter Notebook
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
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Mar 18, 2025 - Python
(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"
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Apr 1, 2024 - Python
CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
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Jul 8, 2023 - Jupyter Notebook
single cell foundation model for Gene network inference and more
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Mar 18, 2025 - Jupyter Notebook
Count-Ception: Counting by Fully Convolutional Redundant Counting
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May 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
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Mar 15, 2025 - MATLAB
Integrated Cell project implemented in pytorch
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Jul 6, 2023 - Python
Cell cycle inference in single-cell RNA-seq
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Apr 25, 2023 - Python
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
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Mar 10, 2025 - Jupyter Notebook
Detect morphological motifs, such as blebs, filopodia, and lamellipodia, from 3D images of surfaces, particularly images of cell surfaces.
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Mar 15, 2025 - MATLAB
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.
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Mar 15, 2025 - MATLAB
Automated Cell Toolkit
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Dec 15, 2020 - Python
Transform 3D cell surfaces into different representations including topographic maps, 3D spheres, and 2D images for doing optimized quantification, data analysis and machine learning.
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Nov 4, 2024 - Jupyter Notebook
3D shape analysis using deep learning
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Oct 19, 2023 - Python
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…
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Jul 18, 2022 - R
Explainable AI model of cell behavior
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Apr 4, 2023 - Python
Communitiy-based Cell Line Ontology
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Jun 24, 2024 - Shell
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