Electron microscopy

Hot-Knife is a library specifically designed for FIB-SEM data and thick sections, which includes code for flattening, deformable alignment with features and a more robust kind of block-matching, and some visualization, manual correction, and import and export tools (n5).

A collection of Java tools and HTTP services (APIs) for rendering transformed image tiles that includes:

• a JSON data model for render, tile, and transform specifications,
• a Java stand-alone render application / library,
• a set of render web services that provide RESTful APIs to persisted collections of tile and transform specifications, and
• a set of Java clients for processing/rendering data that utilize the render web services to retrieve and/or store persisted specifications.
• Docker packaging for building the libraries and deploying the render web services

The basic concept is to render images (tiles) based on transformation files, without having to store the big generated image from an alignment of tiles (mosaicking).

webKnossos is an open-source data sharing and annotation platform for tera-scale 2D and 3D image datasets.

The core features of webKnossos are:

• fast 3D data streaming
• share links to specific locations in the data
• uniquely fast skeleton annotation (flight mode) and
• efficient volume annotation
• mesh rendering
• collaboration and sharing tools

webKnossos facilitates image analysis workflows on multi-terabyte datasets, including visualization of raw and multi-modal microscopy data, distributed training data generation and proof-reading of automatic segmentation.

As a scientific resource, webknossos.org serves as a database for published image datasets including their annotations.

MoBIE (Multimodal Big Image Data Exploration) is a framework for sharing and interactive browsing of multimodal big image data. The MoBIE Fiji viewer is based on BigDataViewer and enables browsing of MoBIE datasets. 

It is also called Platybrowser, and uses the n5 format.

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.