Cytomine open-source release

[Raphael.Maree.]

Dear colleagues and OpenSlide fans,


After five years of research and development at the University of Liège,
Belgium, we are happy to announce to the release under an open source
licence of our Cytomine software (http://www.cytomine.be/)
for collaborative analysis of multi-gigapixel imaging data.


Although our initial focus was on biomedical research with cytology and
histology whole-slide images, this is a generic software that might be
useful for other types of imaging data from various fields (e.g. botany,
geology, astronomy, environmental biology, ...). 


Based on modern web, database, and machine learning algorithms, it has
been designed to foster active and distributed collaboration between
computer vision/machine learning researchers and other scientists
dealing with very large images.


Among other functionalities, it implements:
- a web user interface to explore (à la Google Maps) very large images
using OpenSlide for digital slide scanner pyramidal formats, and a
combination of VIPS and BioFormats for other (microscopy) formats;

- web user interfaces to efficiently and collaboratively build large
semantic ground-truth datasets from multi-gigapixel images; 

- a multi-thread implementation of our tree-based learning recognition
algorithms (for content-based image retrieval [MIR2010], object
classification [PatternRecognitionLetters2016], image segmentation
[VISAPP2009], and landmark detection;

- web proofreading tools to edit (ours or yours) algorithm predictions;

- a RESTful API and software templating mechanisms to easily
import/export data with your own software and extend it to your own
purposes;

- Python and Java clients to easily access and extend the system. 


Our paper in Bioinformatics (open access):
http://bioinformatics.oxfordjournals.org/content/early/2016/01/09/bioinformatics.btw013.full.pdf+html

Other related papers:
http://www.cytomine.be/#publications

Read more (documentation, source code, etc.) on:
http://www.cytomine.be/


Best regards,
Raphaël.
-- 
Raphaël Marée (PhD)
http://www.montefiore.ulg.ac.be/~maree/
http://www.cytomine.be/
Tél.: +32 4 366 26 44 | Fax: +32 4 366 29 84