Data handling


Orthanc aims at providing a simple, yet powerful standalone DICOM server. It is designed to improve the DICOM flows in hospitals and to support research about the automated analysis of medical images. Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol.

Orthanc can turn any computer running Windows, Linux or OS X into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight and standalone, meaning that no complex database administration is required, nor the installation of third-party dependencies.

What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc.

Orthanc also features a plugin mechanism to add new modules that extends the core capabilities of its REST API. A Web viewer, a PostgreSQL database back-end, a MySQL database back-end, and a reference implementation of DICOMweb are currently freely available as plugins.


ClearMap is a toolbox for the analysis and registration of volumetric data from cleared tissues.

It was initially developed to map brain activity at cellular resolution in whole mouse brains using immediate early gene expression. It has since then been extended as a tool for the qunatification of whole mouse brain vascualtur networks at capilary resolution.

It is composed of sevral specialized modules or scripts: tubemap, cellmap, WobblyStitcher.

ClearMap has been designed to analyze O(TB) 3d datasets obtained via light sheet microscopy from iDISCO+ cleared tissue samples immunolabeled for proteins. The ClearMap tools may also be useful for data obtained with other types of microscopes, types of markers, clearing techniques, as well as other species, organs, or samples.

ClearMap SCreenshot

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:

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).