Digital Histology Interest Group or DHIG

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National repository of virtual slides?

  • 1.  National repository of virtual slides?

    Posted 07-17-2014 11:20
    The idea of sharing virtual microscopy resources has been brought up from time to time in published articles and informal discussions among histologists.  Is a national repository of virtual slides where any course or program director could obtain slides a good idea?  What would be the best way to create such a resource?  What are the impediments to creating such a resource?
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    Robert Ogilvie
    Professor Emeritus
    Medical University of South Carolina
    Mount Pleasant SC
    843-693-1065843-693-1065
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  • 2.  RE: National repository of virtual slides?

    Posted 07-17-2014 12:58

    Hello,

    I'd definitely be interested in such a resource, and in helping to set it up/look for funding sources etc..  I think it is important to have access to a wide variety of slides, including more variability than possible in a single slide collection.  Many of us have informally traded slides here and there for this reason.  It would need to be possible for people to physically download the files and then utilize them in their own viewers in order to be most useful.  This way, faculty could incorporate the slides into exams or lessons, annotate them etc... using their own viewers and tools. 

    Issues to consider include copyright (e.g. would home institutions be willing to share including downloads); file format (would need to be downloadable in a format that could easily be converted to other formats); server space and bandwidth.  How would it be accessed (e.g. limit to AAA members through their website thus having a degree of password protection vs create own site that is membership accessed).

    I'm sure their are more issues that others can add.

    Haviva

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    Haviva Goldman
    Associate Professor
    Drexel University College of Medicine
    Philadelphia PA
    215-991-8467
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  • 3.  RE: National repository of virtual slides?

    Posted 07-18-2014 09:24
    I just wanted to chime in that we would also be interested in the availability of such a resource and have virtual slides we'd be willing to contribute. Ours were scanned by Aperio some years ago. I'm not an expert at other formats for such slides and wonder if slides would have to be catalogued by format for ready access and whether format conversion is either necessary or desirable.

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    Douglas Paulsen
    Professor, Associate Dean
    Morehouse School of Medicine
    Atlanta GA
    404-752-1559
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  • 4.  RE: National repository of virtual slides?

    Posted 07-19-2014 18:06
    This sounds like a great idea, but are the materials copyright protected. Would we be able to create a database from it?
    If so, then would AAA be responsible for "management" of the images?

    Just wondering how to move forward.

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    Linda May
    Assistant Professor
    East Carolina University
    Greenville NC
    252-737-7072
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  • 5.  RE: National repository of virtual slides?

    Posted 07-20-2014 11:27
    I think this is a great idea. As someone who has been involved with making the digital histology of embryos available here are a few of the things I think need to be considered.

    Copyright - All images put in the repository should be freely available for anyone's use. copyright could stay with the original owner or could be assigned to an organization. There should be a user agreement ( license ) that users agree to before downloading images. It should probably restrict the commercial use of the images without permission of the copyright holders.

    Format - Aperio images seem to be commonly used but they are a proprietary format and their use restricts the applications of the images and limits the use to those who have the server software. I would suggest that there be different parts of the repository for different formats; aperio, jpg, png etc so images are available to the widest possible audience.

    Management - storage space and bandwidth are likely to be major consideration and cost - unless funding can be obtained from somewhere like NLM then it is probably best if an organization like AAA  take the lead.

    Continuity - The need for constant maintenance, updates and backup means that if you want this repository to be available indefinitely these aspects of it should be the responsibility of an organization like AAA rather than a single institution.

    I would be happy to help with this project in any way I can. I would also be happy to contribute all the Virtual Human embryo section images.

    John   

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    John Cork
    Assoc. Professor
    LSUHSC
    New Orleans LA
    504 568 7177
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  • 6.  RE: National repository of virtual slides?

    Posted 07-21-2014 10:22
    I may be mistaken, but for us the Aperio images are accessible through software (ImageScope) that can be downloaded for free from the Aperio website. http://www.leicabiosystems.com/index.php?id=8991 

    I agree with John that any images in such a repository should be easily and freely accessible. I also agree that management and maintenance are issues that should be dealt with up front.

    -------------------------------------------
    Douglas Paulsen
    Professor, Associate Dean
    Morehouse School of Medicine
    Atlanta GA
    404-752-1559
    -------------------------------------------




  • 7.  RE: National repository of virtual slides?

    Posted 07-21-2014 13:16

    Hello John, you've done a terrific job on covering all the important features of the proposed Histology database.  I might add that the Human Anatomy and Physiology Society (HAPS) has a Histology database at http://hapshistology.wikifoundry.com/ (check out Slide Box) that is managed by Bill Karkow (wkarkow@dbq.edu).  On the HAPS homepage at http://www.hapsweb.org/, he also has a Histology Challenge section on the Teaching Resources page that shows from time to time an unknown Histology image for identification and discussion (great idea for adding interactivity and group learning). 

    I think that having still images of various magnifications and formats would suffice for those of us who do not have the Aperio software so I agree that it might be useful to think in terms of Aperio and non-Aperio access modes. 

    My own interest area at this time is in making 3D printed tactile learning objects so that blind or visually impaired students can learn by touch and feel what sighted students see when looking into a microscope.  So, I would suggest that the database include the 3D print files (stl format) for anyone interested in making a 3D printed tactile learning object.  I've had early discussion with the HAPS group for use of their images in making an stl file database so if any Virtual Histology database emerges from our discussions, it could also serve as a way to make available the files needed for 3D printing the images.

    Mike   

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    Michael Kolitsky
    Online Adjunct Professor
    The University of Texas at El Paso
    Ocean City NJ
    609-399-2431
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  • 8.  RE: National repository of virtual slides?

    Posted 07-21-2014 14:06

    Thank you, Bob, for bringing this topic to our attention.
    Haviva, John, Doug and Linda have added important aspects to the discussion. Many institutions do not have the resources to generate a comprehensive collection of virtual images and sharing is a great idea. However, as all of you already pointed out, there are a few issues and problems that need to be solved.

    First, creating a national or even better international database needs a financial and technical framework that is probably beyond a single institution. It would make sense to get AAA, NIH or NSF support for this.

    The other problem raised by Linda and others is the copyright issue. One possible solution would be to publish the various virtual slide collections under a Creative Commons License (http://creativecommons.org). That means the copyright stays with the original creator of the resource, but users are allowed to use the collection with specific limitations (At U of Michigan we are using non-commercial, attribution and share alike; http://creativecommons.org/licenses/by-nc-sa/3.0/). There are several different Creative Commons Licenses and that may complicate the issue.

    There is a worldwide interest in switching to virtual microscopy for histology, embryology and pathology instruction. Many of the requests I am getting for sharing our virtual slide collection are from universities all over the world. Especially new medical and dental programs are interested to instruct their students using virtual microscopy and not to acquire expensive microscope and slide sets. Any solution should therfore include "customers" from non-US countries, specifically third world countries.

    As temporary solutions, besides our open website (http://histology.med.umich.edu/schedule/medical), our virtual slides are accessible (but not downloadable) from the image database of the American Society for Cell Biology (called The Cell, an image library: http://www.cellimagelibrary.org) and I also have created a local, password-protected server here at the University of Michigan from which colleagues, who contact me to request access, can download our collection (about 200 GB). The second solution has worked for colleagues in the US and Europe, but may not be feasible for locations with a slow Internet speed. I have used mailing of a small portable hard drive for countries with slow or unstable Internet connections. However, after my hard drive spent several months in Brazilian customs, I am trying to avoid this option. Therefore, delivery of large datasets is another, more technical concern.

    I'd be happy to join the effort of a national/international virtual slide database and like to offer our/my experience in sharing virtual slide collections.

    All the best

    Michael



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    Michael Hortsch
    Associate Professor
    University of Michigan
    Ann Arbor MI
    734-647 2720
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  • 9.  RE: National repository of virtual slides?

    Posted 07-21-2014 11:10
    I also agree that a centralized repository would be wonderful. 

    The copy right issues, server, bandwidth, management and other concerns brought up by John and Haviva are dead on. 
    The most costly item in this might be the server & management logistics.  I am not sure what type of IT infrastructure AAA has and whether it would be open (and possible) to hosting a massive image data set for AAA members to access - I will inquire with Donovan and report back. 

    We should also look at whether there are any grant opportunities we can explore as a group to make this happen.  Does anyone know of any RFPs that we may look into?  NLM? AAA?


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    Lisa Lee
    Associate Professor
    University of Colorado School of Medicine
    Aurora CO
    303-724-7460
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  • 10.  RE: National repository of virtual slides?

    Posted 07-21-2014 19:01
    It is inspiring to see all of your enthusiasm and willingness to share your resources and expertise!  I pale in comparison to many of your experience and expertise, but I am committed to sharing my digital library and anything else I can contribute to this effort. 

    I think the best approach might be for us to collectively put together a project plan or blue-print of some sort then go from there.  This might help us get a sense of feasibility, scale and other technical issues.  This should also help us put together funding/grant proposals when there are opportunities.  In fact, I was reminded by Shawn Boynes that AAA is rolling out Innovations Grant Program (upto $50,000 per award) in August - we can and should look into this. 

    As for the project blue-print, we could start by filling out the following areas as a group or have a conference call to organize efforts among interested individuals.  Thoughts?

    Project Title:

    Personnel:

    Background & Rationale:

    Project Goals (or Missions):

    Materials & Methods:

    Budget:


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    Lisa Lee
    Associate Professor
    University of Colorado School of Medicine
    Aurora CO
    303-724-7460
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  • 11.  RE: National repository of virtual slides?

    Posted 08-01-2014 12:21

    Hello,

    Tough time of year to keep discussions going with vacations and the new academic year looming very close, but did notice the call for proposals for the innovation grant, so thought I'd just post and see if we can continue the discussion.  The grant seems like a good starting point.  Perhaps a good way to get things started might  be a google doc to share based on Lisa's outline?  I can set one up if others are on board.

    Haviva


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    Haviva Goldman
    Associate Professor
    Drexel University College of Medicine
    Philadelphia PA
    215-991-8467
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  • 12.  RE: National repository of virtual slides?

    Posted 08-04-2014 10:46
    Yes, let's get this ball rolling!  Haviva, thanks for offering to get a shared google doc started, my gmail account is LLeeBio@gmail.com
    I will start filling in the outline with a draft of each section shortly, so that we have a starting point. 

    I am also going to start a new thread for working on the innovation grant so all related discussions can occur there. 

    -------------------------------------------
    Lisa Lee
    Associate Professor
    University of Colorado School of Medicine
    Aurora CO
    303-724-7460
    -------------------------------------------




  • 13.  RE: National repository of virtual slides?

    Posted 08-05-2014 10:44

    Thank you Lisa and Haviva to get the ball rolling.

    I also spent this weekend thinking about the project. As outlined by Lisa, the physical housing of the collection may be a major problem. I am not sure that AAA would be able to take over the management of the virtual slide collections and to provide IT support. Therefore, I would offer to find out whether the University of Michigan could act as the host for the international virtual slide repository. As I outlined in a previous email, we have a system in place that has worked well for our 200 GB Michigan slide collection. Here are a few practical ideas/suggestions: We already have in place a system of server accounts called M+box. Each account has up to 200 GB in space and each of the various donated virtual slide collections regardless of their file type would have its own M+box. Besides a local administrator, a representative of the donor institution would have downloading ability and new slides could be added as they become available. National and international colleagues who want to download a collection would be given reader-only access to the requested M+box, allowing them to download the specific collection. This would work for people with a fast Internet connection and I had colleagues from England, The Netherland and the US successfully using this system for our virtual slide collection. For colleagues without a suitably fast Internet connection, the resources could be downloaded on a small external hard drive and mailed directly by FedEx or airmail. Recently, I used this more old fashioned method for colleagues in Brazil and Saudi Arabia. After copying the hard drive content, they would mail it back.

    We would need a website that could be part of the AAA website. There appears to be an agreement that a permission of the copyright holder in combination with a Creative Commons License would be an excellent solution. We would still need to come up with a viable recharge system to keep the repository open, even after the grant funds have eventually dried up.

    I just talked with my chair and she was supportive that we here at the University of Michigan should be able to provide a physical home for the international repository. I am confident that I can get support from our Dean's office and I have an email in with our Medical School's chief IT person. If I can get him on board to provide IT support, I feel confident that we have a workable infrastructure.

    Lisa and Haviva, I will contact you separately and give you access to the Michigan collection (M+box) and you can take a look and test it out. Bob Oglivie is already a user and has downloaded our collection.

    Please let me know if this is a viable option to proceed and whether I should continue to solicit local support.

    Awaiting your input

    Michael



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    Michael Hortsch
    Associate Professor
    University of Michigan
    Ann Arbor MI
    734-647 2720
    -------------------------------------------




  • 14.  RE: National repository of virtual slides?

    Posted 08-05-2014 11:39
    I just checked out M+ box and it just might be an ideal setup for the repository.  Thank you Michael, for looking into the possibility of the IT infrastructure at U of M as a viable host for the (inter)national repository of virtual slides!  It is also encouraging that your administration is supportive of this effort!  Please keep us posted on what your chief IT person says.  This is wonderful progress already! 

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    Lisa Lee
    Associate Professor
    University of Colorado School of Medicine
    Aurora CO
    303-724-7460
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  • 15.  RE: National repository of virtual slides?

    Posted 08-06-2014 10:16
    Michael, I like what you described as a repository model that is already serving you and your colleagues in other countries.  I might add that if there is interest in making 3D prints of 2D slide images for use by the blind or visually impaired student to learn by touch and feel what sighted students see when using a microscope, the repository model you describe could also serve as a site for storage of the stl files required for 3D printing.  I suspect there would not be much of a call for 3D printed tactile learning objects at the medical school level but it would be of value at the undergraduate and also high school level and might also be a way to bring attention to AAA for making resources available for students studying micro-anatomy who are blind or visually impaired or who also may be kinesthetic learners who learn better when they can touch what they study.  Thanks again for suggesting a very workable model for the repository.

    Mike

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    Michael Kolitsky
    Online Adjunct Professor
    The University of Texas at El Paso
    Ocean City NJ
    609-399-2431
    -------------------------------------------




  • 16.  RE: National repository of virtual slides?

    Posted 08-07-2014 09:42
    Thank you, Mike, for adding to the discussion. From a technical standpoint, the solution I have suggested would be able to distribute any type of file format. Currently the size of our M+box server accounts is 200 GB, which is just big enough to house the Michigan virtual slide collection. The major bottleneck is the Internet speed of the downloader. I am not sure how big 3D and 2D slide files are, but I think the repository has the potential to include technologies like the one you are describing. As a starting point we should first establish a repository for virtual histology (and pathology?) files. Once this is working, I am in favor that we should consider expanding to other electronic resources and teaching tools.
    I am glad that things come together for the grant application and I think we have a good group of interested people who are willing to contribute.
    All the best
    Michael from Michigan


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    Michael Hortsch
    Associate Professor
    University of Michigan
    Ann Arbor MI
    734-647 2720
    -------------------------------------------




  • 17.  RE: National repository of virtual slides?

    Posted 08-14-2014 16:47
    Hello all,

    As an update, I, Haviva and Michael Hortsch are currently working on putting together a AAA innovation grant proposal for establishing an international virtual histology repository.  At this time, we would like to know: who has existing virtual slide collections (regardless of the format) and is willing to make them available through the repository?  Please let us know by posting here or by emailing me. 

    Also, we have restricted access to our proposal on google doc at this time.  If you would like to contribute to the grant proposal and application process itself, please let me or Haviva know asap.

    Thank you!  I know many of us have started teaching already, hope everyone is off to a great start!
    Lisa

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    Lisa Lee
    Associate Professor
    University of Colorado School of Medicine
    Aurora CO
    303-724-7460
    -------------------------------------------






  • 18.  RE: National repository of virtual slides?

    Posted 08-18-2014 10:10
    Hi,

    My apologies for not being able to participate as much as I want to - with med school in full session and the second run of a new, integrated curriculum - this isn't my favorite time of the year. I just wanted to add that I have about 120 scanned digital slides (Aperio platform) in our database (HistoWeb@USD) which are made available to students and teaching faculty and are password protected. I am willing to share these as a part of the project and would be more than willing to help with anything I am able to for successful implementation of the novel idea.

    Thanks,

    Manas

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    Manas Das, M.D.
    Course Director, Medical Histology & Human Embryology
    Assistant Professor, Gross Anatomy & Neuroscience
    Sanford School of Medicine, University of SD
    Vermillion SD
    714-454-0677
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  • 19.  RE: National repository of virtual slides?

    Posted 08-18-2014 15:50
    Thank you, Manas, 
    for expressing your willingness to share. We will add you to a list of prospective donors and we will contact you once we have funding for the project and are able to accept donations. 
    All the best with your teaching. I and probably many others know what you are talking about. This is a busy time of the year for us.
    Michael

    -------------------------------------------
    Michael Hortsch
    Associate Professor
    University of Michigan
    Ann Arbor MI
    734-647 2720
    -------------------------------------------