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.

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Posted in News   •  

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

How to add a segmentation to an image

Add a segmentation to a dataset

1.Login and go to the Upload page, upload your dataset

2.Go to MyVSD->Unvalidated Data

1_unvalidated

3.Deselect the data you don’t want to validate

2_unselect

4.Select the segmentation and press the validate button

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5.Now edit the file information, make sure you add the anatomical region

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6.Now go the the related data tab and search for the source dataset of your segmentation: eg 559 and add it. This creates the relation (link) between the uploaded segmentation and the source dataset

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7.Fill permission/license if needed and go to the Publish tab.

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8.Click on publish. Once finished, your segmentation is now in the system and in your MyVSD-MyData folder

API: Linking

Linking Example

In this example, we use Fiddler to execute the commands.

  1. We want to first check the existing links of a object
  2. Then we create a new link
  3. We can check the existance of the new link
  4. Delete the link

Preparation

Header:

This it the header configuration: Put it in the composer tab -> Parser: in the field below the GET / URL input.

Check existing links

First get the object

GET https://demo.virtualskeleton.ch/api/objects/110

We get the 200 Http response code in the Session List and click on the entry in the list to view the JSON output. We check if the desired object is already linked.

if not, we can send the URLs of both objects to create a link using POST

Create a link:

  1. Add this line to the header Content-Type: application/json

  1. The POST endpoint to create the link is

POST https://demo.virtualskeleton.ch/api/object-links

with the Request Body containing both selfUrl’s of the objects (eg. 110, 86):

you get back the object-links id selfURL in the response:

selfUrl=https://demo.virtualskeleton.ch/api/object-links/102

check if the link is present in object 110 using again

GET https://demo.virtualskeleton.ch/api/objects/110

Deleting an existing link

You need to identify the ID of the link. This information is in the object as linkedObjectRelations. To delete to link just use:

DELETE https://demo.virtualskeleton.ch/api/object-links/102