3D

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).

Phindr3D is a comprehensive shallow-learning framework for automated quantitative phenotyping of three-dimensional (3D) high content screening image data using unsupervised data-driven voxel-based feature learning, which enables computationally facile classification, clustering and data visualization.

Please see our GitHub page and the original publication for details.

The tool allows to measure the area of the invading spheroïd in a 3D cell invasion assay. It can also count and measure the area of the nuclei within the spheroïd.

Local Z Projector is an ImageJ2 plugin, available in Fiji, that can perform local-Z projection of a 3D stack, possibly over time, possibly very large.

LZP performs projection of a surface of interest on a 2D plane from a 3D image. It is a simple tool that focuses on usability and is designed to be adaptable to many different use cases and image quality.

• It can work with 3D movies over time with multiple channels.
• It can work with images much larger than available RAM out of the box.
• It takes advantage of computers with multiple cores, and can be used in scripts.

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.