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=Call for Datasets for the EM Segmenter Use Case Library=

Let us help you turn your segmentation problem into a success story. If you have an interesting segmentation problem that is not yet covered in the [[EMSegmenter-Tasks| library ]], send us your case: we will try to segment it for you and design a tailored segmentation approach you can use. We then add the anonymized data to the library and build a guided step-by-step tutorial for it. This is a time and resource limited service available until July 1, 2011. <br>
If interested drop a line to '''Dominique.Belhachemi at uphs.upenn.edu''' or '''Kilian.Pohl at uphs.upenn.edu'''

=What You Will Need To Do=

* just send us an Email with a brief description of the problem
* send us your image data with the corresponding (manual) segmentation. Please provide more than 10 instances, so that we can generate a robust atlas. Please also insure that the data can be publicly distributed
* save your image data as NRRD or NIFTI files
* if you are unsuccessful in saving the data as described above (which is the anonymization), see our  [http://wiki.na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:Anonymization Anonymization Instructions] , or let us know and we'll walk you through it.

=What We Will Do=

* based on your segmentations we will create an atlas
* we will create a 3DSlicer scene with optimized EM Segmenter parameters for your use case
* we will send you the final result as well as the procedure and parameters
* we will add your use case (3DSlicer scene + atlas data) to our [[EMSegmenter-Tasks|Segmentation Task Library]] which will become part of a future 3DSlicer version
* this will contain parameters for a successful segmentation which you can load directly into slicer and apply on your data
* this page will also contain a description of your segmentation problem, the exact workflow of obtaining the segmentation, an acknowledgment of your lab and links to your institution and related research paper 
* if you can provide us with criteria that define a good segmentation, we will use them in optimization efforts.
* [[ EMSegmenter-Tasks:MRI-Human-Brain-Parcellation | example of what the final shared product will look like ]]

=Limitations/Disclaimer=

* we can assist only with 3DSlicer software.
* this is a time-limited service, available in a first trial until 'July 1, 2011.
* depending on workload, we try to get you something within a few weeks, but we cannot guarantee a particular result or a specific turnaround time.
* all shared data-sets are anonymized. Sharing anonymized data in most cases is IRB exempt based on Code of Federal Regulations 45 CFR 46.101(b), which lists as exemption category 4:

    Unless otherwise required by department or agency heads, [...] the following categories are exempt [...]: 
    
    4.Research involving the collection or study of existing data, documents, records , pathological specimens, 
    or diagnostic specimens, if these sources are publicly available or if the information is recorded by the 
    investigator in  such a manner that subjects cannot be identified, directly or through identifiers linked 
    to the subjects.