+----------+-----------------------------------------------------------+
| ### *    | ### **TBPT Workspace Teleconference**                     |
| *Meeting |                                                           |
|  Title** |                                                           |
+----------+-----------------------------------------------------------+
| #        | ### **October 15, 2007 / 12 to 1 PM (ET)**                |
| ## **Dat |                                                           |
| e/Time** |                                                           |
+----------+-----------------------------------------------------------+
| ### **Su | ### **Fred Prior provided the "Tissue Ban                 |
| mmary (i | ks & Pathology Tools" Workspace Teleconference participan |
| n Bullet | ts a summary of the Imaging Workspace's activities, with  |
|  Point f | an emphasis on the NLST / Pathology Informatics Project** |
| ormat)** |                                                           |
|          | ### **The workspace was put in place t                    |
|          | o establish the necessary tools for radiology imaging --  |
|          | and then use those tools in the broader imaging context** |
|          |                                                           |
|          | ### **Efficient bulk data transp                          |
|          | ort has been added by the IVI Middleware team to caGrid** |
|          |                                                           |
|          | ### **DICOM capability h                                  |
|          | as also been added to the Grid-- not all of DICOM is in c |
|          | aDSR yet, but there is enough of a set to be functional** |
|          |                                                           |
|          | ### **The Testbed group has created several demons        |
|          | trations for the tools of the workspace; these kinds of d |
|          | emonstrations help in the evolution and evaluation of the |
|          |  imaging tools; the grid package is available on GForge** |
|          |                                                           |
|          | ### **NCIA Summary:**                                     |
|          |                                                           |
|          | ### **- not a caBIG^TM^ program (predated t               |
|          | he Imaging Workspace), but has been adopted as the primar |
|          | y image repository (images mostly from RIDER and LIDC)**  |
|          |                                                           |
|          | ### **- contains a total of 1.7 million images**          |
|          |                                                           |
|          | ### **- NCIA is growing, and h                            |
|          | as the ability to be instantiated at multiple locations** |
|          |                                                           |
|          | ### **- version 3 of                                      |
|          | NCIA has a full grid interface and full grid federation** |
|          |                                                           |
|          | ### **gACRIN Summary:**                                   |
|          |                                                           |
|          | ### **ACRIN is an imaging core that grew out of the Am    |
|          | erican College of Radiology (ACR), which supports a large |
|          |  of number of clinical trials; a subset of these (1000 ca |
|          | ses from a DNIST study) are being made available at their |
|          |  NCIA instance, which is the 2^nd^ instance of the NCIA** |
|          |                                                           |
|          | ###                                                       |
|          | **ACRIN has taken their proprietary data elements and exp |
|          | osed them on the grid via incorporating them into caDSR** |
|          |                                                           |
|          | ### **MIRC Field Center is used to extract images from    |
|          | their warehouse and insert them into the exposed subset** |
|          |                                                           |
|          | ### **AIM Summary:**                                      |
|          |                                                           |
|          | ### **AIM allows the user to make annotations tie         |
|          | d to a standard vocabulary (such as SNOMED) -- annotation |
|          | s allow the explanation of the information in the image** |
|          |                                                           |
|          | ### **exchang                                             |
|          | ing annotations is currently difficult because of their p |
|          | roprietary use (exchanging markups is less challenging)** |
|          |                                                           |
|          | ### **RadLex Research Playbook -- involves the ide        |
|          | ntification of terms to use as a norm in radiology imagin |
|          | g, and then adding them into caDSR (AIM ties into this)** |
|          |                                                           |
|          | ### **AVT Summary: the g                                  |
|          | oal is to develop a database of AIM annotations -- this p |
|          | roject is a way to measure change over time (allows more  |
|          | accurate determination of "truth") (AIM ties into this)** |
|          |                                                           |
|          | ###                                                       |
|          |                                                           |
|          | ### **AIM also ties into XIP:**                           |
|          |                                                           |
|          | ### **AIM and Middleware come together to create an envi  |
|          | ronment for visualization and image analysis, enabling th |
|          | e accessing of grid analytic services and data services** |
|          |                                                           |
|          | ### **the                                                 |
|          | cornerstone of XIP is the XIP Tool Builder -- this applic |
|          | ation is used by using libraries that have been wrapped i |
|          | nto the builder (VTK and ITK are the wrappers utilized)** |
|          |                                                           |
|          | ### **XIP                                                 |
|          | applications are built with the XIP Tool Builder -- the a |
|          | pplications are written completely platform independent** |
|          |                                                           |
|          | ### **the                                                 |
|          |  plug -- in interface comes from the DICOM WG 23 effort** |
|          |                                                           |
|          | ### **the purpose                                         |
|          | of the grid interface is to provide data and grid analyti |
|          | c services, not to take the web interface and export it** |
|          |                                                           |
|          | ### **there are three parts -- a host and application, co |
|          | nnected by a plug-in interface; the host allows the acces |
|          | s of data from various data sources, and allows the launc |
|          | h of an application; when an application is launched, the |
|          |  host feeds the information into a plug -- in interface** |
|          |                                                           |
|          | ### **the c                                               |
|          | urrent host is made for developers -- a clinical research |
|          |  user host (which should be ready for demonstration by RS |
|          | NA 2007) is being developed for a more typical end user** |
|          |                                                           |
|          | ### **NLST / Pathology Informatics Project:**             |
|          |                                                           |
|          | ### **A project to va                                     |
|          | lidate spiral CT over chest radiographs, looking at the s |
|          | pecificity and sensitivity of both tests to lung cancer** |
|          |                                                           |
|          | ### **The c                                               |
|          | ommittee wanted to collect pathology samples and analyze  |
|          | the data as digital images (after the clinical trial) --  |
|          | the goal of this 9 week project is to build a prototype** |
|          |                                                           |
|          | ### **caTissue suite is used to track and guide the coll  |
|          | ection of material (from 4 selected screening sites -- Pi |
|          | tt, UCLA, OSU, and Wash. U.) -- taking whole slide images |
|          |  (commercial vendor is used for digitization) and managin |
|          | g that data in the NCIA (at the Wash. U. NCIA instance)** |
|          |                                                           |
|          | ### **the project is a web based porta                    |
|          | l allowing access to caTissue suite and online querying** |
|          |                                                           |
|          | ### **rather than XIP, caMicrosco                         |
|          | pe (developed at OSU) is being used as the image viewer** |
|          |                                                           |
|          | ### **the prot                                            |
|          | otype is going to process \~1.5 terabytes of image data** |
|          |                                                           |
|          | ### **QUESTIONS / ANSWER SESSION:**                       |
|          |                                                           |
|          | ### **Has XIP been experimented with in                   |
|          |  using whole slide images? Why was it not used in NLST?** |
|          |                                                           |
|          | ###                                                       |
|          |                                                           |
|          | > **The main issue is data format, as the slides come     |
|          | > from a digitization company in proprietary format, so   |
|          | > we are trying to decide (for the prototype) what the    |
|          | > correct format is; XIP can be built to do this, but     |
|          | > caMicroscope was ready for use in this prototype; the   |
|          | > Imaging Workspace is assuming that pathologists want a  |
|          | > "Google Earth" type viewer**                            |
|          |                                                           |
|          | 1)  **It seems that XIP is heavily tied into WG 23 --     |
|          |     does the WG 23 standard address pathology imaging in  |
|          |     any way?**                                            |
|          |                                                           |
|          | > **The WG23 interface is designed to work at any kind of |
|          | > work station -- it gives us a convenient way of moving  |
|          | > an application from one environment to another.         |
|          | > Although there is nothing pathology specific, the WG 23 |
|          | > standard is fairly general to imaging whereas it should |
|          | > support pathology imaging.**                            |
|          |                                                           |
|          | 2)  **Users can use the NLST portal to access caTissue -- |
|          |     are they actually taken into the caTissue user        |
|          |     interface?**                                          |
|          |                                                           |
|          | > **Yes -- they are. An instance of caTissue has been set |
|          | > up at Wash. U. for this project specifically.**         |
|          |                                                           |
|          | 3)  **Will the links within caTissue (to open images)     |
|          |     only work within the local instance, or at all        |
|          |     instances?**                                          |
|          |                                                           |
|          | > **Although only the local Wash. U. instance will work   |
|          | > for the prototype, the beauty of NCIA is that it will   |
|          | > allows federated querying (meaning one query searches   |
|          | > all NCIA instances) for other projects if desired. This |
|          | > project, due to a constraint on resources, did not      |
|          | > permit this function.**                                 |
|          |                                                           |
|          | 4)  **How extensible is XIP? How much work would it take  |
|          |     to attach a slide scanner, or image analysis          |
|          |     algorithm? Is that even feasible given the size of    |
|          |     the image?**                                          |
|          |                                                           |
|          | > **The main issue is what format the slide is in after   |
|          | > being digitized. The beauty of XIP is that if there are |
|          | > other open source libraries that are essential, in a    |
|          | > short while they can be integrated into XIP (libraries  |
|          | > written in any language -- Java, C++, etc.); the        |
|          | > bottleneck is understanding data as it comes in -- the  |
|          | > data format (as the workflow for different analyses is  |
|          | > variable); there are no inherent limitations by XIP on  |
|          | > how big an image can be, although the host on which the |
|          | > application is being run may have a size limit**        |
+----------+-----------------------------------------------------------+
| ##       | ###                                                       |
| # **Arti |                                                           |
| facts (E |                                                           |
| mbedded  |                                                           |
| Document |                                                           |
| s, GForg |                                                           |
| e Links, |                                                           |
|  etc.)** |                                                           |
+----------+-----------------------------------------------------------+
| ### *    | ###                                                       |
| *Other** |                                                           |
+----------+-----------------------------------------------------------+

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