Collection

Most of RestoreTools is now bundled with IR tools.

‘’’Squassh’’’ is a tool for 2D and 3D segmentation and quantification of subcellular shapes in fluorescence microscopy images. It provides globally optimal detection and segmentation of objects with constant internal intensity distribution, followed by object-based colocalization analysis. The segmentation computed by Region Competition can optionally correct for the PSF of the microscope, hence providing optimally deconvolved segmentations. Part of the mosaic suite

OMERO is an image database application consisting of a server and several clients, the most important of which are the web client and Insight java application.

Metadata are extracted from images that have been imported (either using the Insight client, or directly from the filesystem), and this is accessible for search. A standardised hierarchy of Project > Dataset > Image in which image thumbnails can be viewed, combined with group membership, tagging, and attachment of results and other files gives a powerful framework for organising scientific image data. Images can also be analysed server-side or client-side within the base OMERO application or one of its many extensions.

OMERO has APIs for extension in multiple languages: java, python, C++ and MATLAB; and such extensions have easy access to the image data and metadata in the database