Repository Index

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

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis

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

A Python interface to access neuroanatomical atlases

• neuroscience
• python
• microscopy
• registration

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

Python package for image-based profiling

• cytominer
• microscopy
• morphological-profiling
• python

An interactive image processing program for biologists written in Python.

• biologists
• python
• imagej
• calcium