Data collections

Collection can now be used to efficiently present, describe and publish a well-defined set of data objects on SMIR. A collection consists of its description and a list of objects stored on SMIR. Having collections and DOIs available, SMIR is ready for your dataset publication.

Collection are create from folders and consist of its description and a list of objects. Please read the smir documentation for detailed information.

Collection are objects, therefore they

  • can have a DOI
  • have meta data
  • have permissions
  • can be searched

Three featured collections are available for the launch of this feature

Use the search tool to display all collection objects

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DOI

SMIR signed an agreement with a DOI Registration Authority (ETH Zurich) to enable attaching a Digital Object Identifier (DOI) to any dataset published on the database. Building and curating data collections is difficult and time consuming. This permanent identifier will increase the visibility of the work by making reference to your datasets easy. Furthermore, the DOI published on SMIR are automatically registered on DataCite – a non-profit website, where these datasets are accessible for search based on their meta-information.

A DOI identifies an object permanently, even if the object changes its location, its owner or other characteristics. The DOI does this through redirection, using the Handle system.

Further resources:

Please read the full documentation at docs.smir.ch

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SMIR supports now MiNIML

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SMIR supports now the upload of

  • GSM – Genomic Sample
  • GSE – Genomic Series
  • GPL – Genomic Platform

in the MINiML (xml) format

MINiML (MIAME Notation in Markup Language, pronounced ‘minimal’) is a data exchange format optimized for microarray gene expression data, as well as many other types of high-throughput molecular abundance data. MINiML assumes only very basic relations between objects: Platform (e.g., array), Sample (e.g., hybridization), and Series (experiment). MINiML captures all components of the MIAME checklist, as well as any additional information that the submitter wants to provide. MINiML uses XML Schema as syntax.[1]

 

 

New Domain for VSD-SMIR

From the beginning, the instance of the Virtual Skeleton Database Framework (VSD) was running at https://virtualskeleton.ch and the development was led by the ISTB, University of Bern.  Almost two years ago, the Swiss Institute for Computer Assisted Surgery (SICAS)  took over the lead. Now this change is also reflected by the domain and the name.

The domain changed to smir.ch and the platform is now called SICAS Medical Image Repository (SMIR)).

Together with the change, a EV SSL Extended Validation Certificate has been acquired for the new domain resulting in the green bar before the URL indicating the certified, verified and encrypted connection using a modern cipher suite for the encryption.  2015-10-14_16-13-20_cropped

Additionally, the front page received an update including sections to get help you get started with the web UI and the REST API.

frontpage

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STL support added

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Users can now upload STL surface model files. The implemented model viewer allows to  preview the structure directly in the browser:

  • Use the left mouse button to rotate
  • The scroll wheel  to scale
  • And the right mouse button to drag the model

 

Statismo CLI interface has arrived in v 0.11.0

The statismo developers have added a command line interface to Statismo and they have released version 0.11.0!

It is now possible to perform the most common shape modelling tasks directly from the command line withou any programming involved.

The initial set of command line features include tools

  • for model building
  • for exploring a model
  • for fitting a model to surfaces and images.

You will find the full list of currently available tools as well as two common use case scenarios on the statismo wiki.

Head over to github to download the statismo CLI or to give feedback to the devs!

A Special thanks goes to Frank Mueller from the University of Basel who developed the initial toolset.

Downloads:

ISLES 2015 Challenge

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We are hosting the 2015 MICCAI Challenge for Ischemic Stroke Lesion Segmentation (ISLES). The SMIR is distributing the multimodal images and offers the online evaluation platform.

The challenge is organized by Oskar Maier (Universität zu Lübeck), Björn Menze (Technische Universität München) and Mauricio Reyes (Universität Bern).

For more information please visit www.isles-challenge.org

To participate proceed to our SMIR ISLES 2015 page

Scientific Data Journal / VSD-SMIR collaboration

VSD-SMIR is now an approved data repository of Scientific Data Journal

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The VSD-SMIR is now included in the list of recommended repositories for Life-science community resources of the Scientific Data Journal. Researchers are invited to upload their data (medical images, labeled images, statistical shape model, and clinical trial data) to the VSD-SMIR. See the biosharing.org entry of the VSD-SMIR for a full list of supported data types.

“Scientific Data is an open-access, peer-reviewed publication for descriptions of scientifically valuable datasets. Our primary article-type, the Data Descriptor, is designed to make your data more discoverable, interpretable and reusable. Scientific Data is the new data journal from Nature Publishing Group.” Scientific Data Repositories

Store your Clinical Trial Data on the VSD-SMIR

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The VSD-SMIR has received support for an additional Dataformat! The CDISC-ODM standard has been included to store Clinical Trial Data. You can now manage Clinical Research Form information together with imaging and precessed data on the VSD-SMIR.

“The CDISC Operational Data Model (ODM), which is maintained by the CDISC XML Technologies Team, is designed to facilitate the regulatory-compliant acquisition, archive and interchange of metadata and data for clinical research studies. ODM is a vendor neutral, platform independent format for interchange and archive of clinical study data … “. CDISC-ODM website