Repository Index

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

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

Automated 3D brain registration with support for multiple species and atlases.

• registration
• atlases
• brain
• neuroscience

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

• biology
• fluorescence
• image-analysis
• image-processing

Gaussian processes and Bayesian optimization for images and hyperspectral data

• image-processing
• hyperspectral-images
• gaussian-processes
• bayesian-optimization

Lattice light-sheet post-processing utility.

• microscopy
• light-sheet
• image-processing
• image-analysis

An interactive image processing program for biologists written in Python.

• biologists
• python
• imagej
• calcium

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

• microscopy
• image-processing
• segmentation
• biology

A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).

• imaging
• microscopy
• contractility
• collagen

#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720

• segmentation
• image-processing
• zebrafish
• vasculature

Panoptic segmentation algorithms for 2D and 3D electron microscopy images

• deep-learning
• semantic-segmentation
• segmentation
• pytorch