Segment Anything for Microscopy
- microscopy-images
- segment-anything
- segmentation
- cell-segmentation
Repository Index
47,133 repositories indexed
1–24 of 47 · Most stars
ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
- histopathology-images
- microscopy
- sliding-windows
- medical-image-analysis
Tools for computational pathology
- machine-learning
- digital-pathology
- computational-pathology
- biomedical-image-processing
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
- ai
- cell
- digitalpathology
- microscopy
Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.
- hubmap
- imaging
- openmicroscopy
- ome-tiff
Image restoration for fluorescence microscopy
Automated 3D cell detection in very large images
- microscopy
- cell-detection
- deep-learning
- image-analysis
Deep and Machine Learning for Microscopy
- microscopy
- materials
- machine-learning
- materials-science
OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.
- omero
- java
- python
- server
Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning
- tensorflow
- python3
- keras
- resnet-101
A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
PyTorch Connectomics: segmentation toolbox for EM connectomics
- computer-vision
- neuroscience
- connectomics
- pytorch
A Python interface to access neuroanatomical atlases
- neuroscience
- python
- microscopy
- registration
Non-comprehensive list of projects and resources related to open microscopy.
Read and write Neuroglancer datasets programmatically.
- neuroglancer
- volumetric-data
- python
- cloud
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.
- python
- microscopy
- scripting
- automation
Interoperable web-based DICOM slide microscopy viewer and annotation tool
Automated 3D brain registration with support for multiple species and atlases.
- registration
- atlases
- brain
- neuroscience
A collection of tools for painting super-resolution images
- microscopy
- super-resolution
- smlm
- dna-paint
Accurate and efficient spot detection for microscopy data
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
Axon/Myelin segmentation using Deep Learning
- deep-learning
- machine-learning
- myelin
- axon
The python-microscopy environment - an open-source package for light microscopy