Segment Anything for Microscopy
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Updated
May 21, 2024 - Jupyter Notebook
Segment Anything for Microscopy
MIC-MAQ for Microscopy Images of Cells - Multi Analyses and Quantifications is an ImageJ/Fiji Plugin for automatic segmentation of nuclei and/or cells for quantifications in other channels including foci detection
Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".
NUCLEI SEGMENTATION USING STARDIST AND PYTHON IN GOOGLE COLAB
StarDist - Object Detection with Star-convex Shapes
StarDist plugin for napari
Feature extraction from GEOJson nuclei and tissue segmentation maps
MICCAI2023 - TransNuSeg: A Lightweight Multi-Task Transformer for Nuclei Segmentation
CompSegNet: An enhanced U-shaped architecture for nuclei segmentation in H&E histopathology images
A PyTorch Implementation of the StarDist Nuclei Segmentation Architecture
Encoder-Decoder Cell and Nuclei segmentation models
ImageJ scripts for: (a) batch opening confocal files with two channels and merging them and (b) for a batch of confocal images with two channels, identifying nuclei as ROIs using one channel and quantifying the mean pixel intensity of each ROI using the other channel, and outputting results in Excel. Requirements and assumptions are in comments.
H&E ROI-Level and WSI-Level Nuclei Segmentation with HoVer-Net
compact version of the official hovernet impl in pytorch
Using Deep Learning techniques for nuclei segmentation. Data extracted from Kaggle competition 2018 Data Science Bowl
Nuclei Segmentation using ResUNet
Nuclei segmentation and classification (Cancer cells)
Performs instance segmentation and classification of nuclei in Multi-Tissue Histology WSIs(generally 100k*100k pixels).
GradMix for nuclei segmentation and classification in imbalanced pathology image datasets: MICCAI 2022
MICCAI-COMPAY-2021: An automatic nuclei image segmentation based on multi-scale split-attention u-net
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