ReMoToo

ReMoToo is a system service that is able to stream the desktop to web remote clients, making it possible to have interactive sessions over remote high performance systems or even regular systems through a standard web browser. The key aspects of ReMoToo are the high quality visualization it provides as well as its low latency. To achieve it, ReMoToo uses video compression on the server side and sends the generated video stream to the client in a transparent and easy way. On the server side, several ReMoToo instances are managed by another service called ReMoLON. This service is in charge of the initiation, control and stop of ReMoToo visualization streams. The ReMoLON system service is connected through the ReMoLON_FrontEnd, a simple web server running on the login node/s. This FrontEnd is in charge of the user authentication and configuration of the ReMoToo instances through the ReMoLON system services.

Other software

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3D Slicer

3D Slicer is: A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy. A free, open source software available on multiple operating systems: Linux, MacOSX and Windows Extensible, with powerful plug-in capabilities for adding algorithms and applications. Features include: Multi organ: from head to toe. Support for multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy. Bidirectional interface for devices. There is no restriction on use, but Slicer is not approved for clinical use and intended for research. Permissions and compliance with applicable rules are the responsibility of the user.

Data analysis and visualisation

3DSpineS

Dendritic spines of pyramidal neurons are the targets of most excitatory synapses in the cerebral cortex and their morphology appears to be critical from the functional point of view. Thus, characterizing this morphology is necessary to link structural and functional spine data and thus interpret and make them more meaningful. We have used a large database of more than 7,000 individually 3D reconstructed dendritic spines from human cortical pyramidal neurons that is first transformed into a set of 54 quantitative features characterizing spine geometry mathematically. The resulting data set is grouped into spine clusters based on a probabilistic model with Gaussian finite mixtures. We uncover six groups of spines whose discriminative characteristics are identified with machine learning methods as a set of rules. The clustering model allows us to simulate accurate spines from human pyramidal neurons to suggest new hypotheses of the functional organization of these cells.

Data analysis and visualisationData

3D Structure Tensor Analysis

A Structure Tensor Analysis (STA) tool for the characterization of local 3D orientation in TIFF image stacks. This tool is based on the evaluation of local image intensity gradients. In addition to the local 3D orientation, it also provides a full analysis of local gradient strength, structure disarray, shape and fractional anisotropy indices.

Data analysis and visualisation

Other software

3D Slicer

3DSpineS

3D Structure Tensor Analysis

Make the most out of EBRAINS