lennyvoneche / cytomine-ims-migration-grails-4

Cytomine IMS

Cytomine Image Management System (Cytomine-IMS) is a web application for image manipulation.

Overview

The goal of this server is to carry image operations and to provide a simple REST API with multiple image formats support. In particular, IMS server provides services to:

• upload an image
• get image thumbs
• extract image tiles
• extract crops

Supported formats

• Pyramidal TIFF (.tif)
• Planar TIFF (.tif)
• JP2000 (.jp2)
• JPEG (.jpg)
• PNG (.png)
• PGM (.pgm)
• DICOM (.dcm)
• BMP (.bmp)
• Aperio (.svs)
• Hamamatsu (.vms, .ndpi)
• Leica (.scn)
• MIRAX (.mrxs)
• Philips (.tiff)
• Sakura (.svslide)
• Ventana (.bif, .tif)
• Huron TIFF (.tif)
• Photoshop TIFF (.tif)
• CZI TIFF (.tif)
• Cell Sens VSI (.vsi)
• Olympus Dot slide
• OME-TIFF (.ome.tif)
• Zeiss (.czi)
• GeoJP2 (.jp2)
• GeoTIFF (.tif)
• Format supported by Bioformats

Install

To install official release of Cytomine-IMS, see @cytomine. Follow this guide to install forked version by ULiege.

It is automatically installed with the Cytomine-bootstrap procedure using Docker. See Cytomine installation documentation for more details.

Develop

Check how to install a development environment for Cytomine.

References

When using our software, we kindly ask you to cite our website url and related publications in all your work (publications, studies, oral presentations,...). In particular, we recommend to cite (Marée et al., Bioinformatics 2016) paper, and to use our logo when appropriate. See our license files for additional details.

• URL: http://www.cytomine.org/
• Logo: Available here
• Scientific paper: Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel. Collaborative analysis of multi-gigapixel imaging data using Cytomine, Bioinformatics, DOI: 10.1093/bioinformatics/btw013, 2016.

License

LGPL-2.1