The BioImage Suite Datatree Tool: Enabling Flexible Realtime Surgical Visualizations

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This paper describes the Datatree module of BioImage Suite, that allows for rapid and flexible reslicing
of images based on a user-defined tree structure that organizes image and transformation data as well as
electrode localizations, image landmarks, and surface objects. This Datatree tool provides abstracted file
loading, allowing for interface with databases, as well as multisubject capabilities, other plugins designed
for specific image modalities, and an incr Tcl based API, allowing users to extend its functionality with
their own plugins.
There is no code review at this time.

minus Good idea, missing some of the details to really evaluate by David Holmes on 09-05-2006 for revision #1
starstarstarstarstar expertise: 3 sensitivity: 5
This paper describes the method of data visualization within the BioImage software. It includes a description of the software tools used to built the Datatree interface as well as applications that one might want to use the datatree tool.


This submission doesn't include addition information such as the software, source or applications for each of the examples. Since this is a description of the tool, there is no description of an evaluation/validation of the tool in the context of the applications.

Open Science:
Once available, this will be open source software available for evaluation by independent investigators; however, it is now only release with registration as beta software. It will also be important to include the code for the specific examples described in the paper as these examples are the applications where the datatree tool is being used.


Use of Open Source Software:
This is built upon open source software (with a couple of small exceptions described in the other paper on the bioimage suite).

Open Source Contributions:
This will be a useful open source software package when fully available.

Code Quality:
Cannot evaluate

Applicability to other problems:
The authors already describe several applications of this tool. There are many more applications in the field.

Suggestions for future work:
Nothing in particular.

Requests for additional information from authors:
Unfortunately, this is a case where the code really needs to be more available. I believe that the authors will eventually get there, but cannot evaluate right now. I hope that the example applications will also be available with the package in order to evaluate their utility as well as the foundation for new applications.

Additional Comments:
[This is a free-form field]

Comment by Xenophon Papademetris: The source code is available. yellow

Just a couple of points.

The source code is now available (and has been for about 10 days) See, Given the presence of the web-page and a detailed manual page we did not think it necessary to add additional appendices. Just like most software packages that have webpages, the webpage is the definitive source of the current state of the software.

Hence the comment "Unfortunately, this is a case where the code really needs to be more available. I believe that the authors will eventually get there, but cannot evaluate right now." does not really apply.

Also the registration step for downloading the code is fairly trivial -- simply register at the forum, there is no checking or approval of any kind. It is more meant to encourage the use of the forum for support.

Regarding data: We need to work on permissions to anonymize and release sample clinical data. The software has been in regular use in the OR for neurosurgery cases for the last 5-6 months or so and we will try to pick a case or two to anonymize and release.
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Keywords: Image Guided Navigation, Vector Vision Link, User Interfaces
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