Fluorescence microscopy

BioImage.IO -- a collaborative effort to bring AI models to the bioimaging community. 

• Integrated with Fiji, ilastik, ImJoy and more
• Try model instantly with BioEngine
• Contribute your models via Github

This is a database of pretrained deep Learning models. 

LOBSTER (Little Objects Segmentation and Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images, i.e. terabytes of data, exceeding workstation main memory.

• 75 workflows available 
• no programming, with GUI
• matlab based 

This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained models to new images.

DeepCell is neural network library for single cell analysis, written in Python and built using TensorFlow and Keras.

DeepCell aids in biological analysis by automatically segmenting and classifying cells in optical microscopy images. This framework consumes raw images and provides uniquely annotated files as an output.

The jupyter session in the read docs are broken, but the one from the GitHub are functional (see usage example )