Donald:
Haviva's solution probably is the one you want. However, for what it's worth, there are other options if something comes up that prevents implementation of Haviva's solution. The downside to the options I've described below is that your slides would need to be converted from the *.svs format into a "Google Maps"-like format; this can be done (see below), but I suspect that it would involve a lot more time & effort than using the Drexel software.
Because we wanted a system that could be distributed freely and that would allow us to display high-resolution multifocal-plane virtual slides (e.g.,
UM130-75), we have been developing a virtual microscope that uses a non-proprietary 2
x-pyramidal tile-architecture similar to that used by Google Maps. The system includes a viewer (
http://viewer.pnwu.edu) which displays the slides, a "slide box" front-end to the database (
http:slidebox.pnwu.edu), a database consisting of the hierarchically-arranged jpg images (the actual slides), and a SQL database (with information about the slides). The software is free (under a
GNU General Public License) and is available on GitHub ... but talk to me before you download it from GitHub since I haven't gotten around to uploading the most current versions. If you want to "play" with the system (or use it for your class), the links to the Viewer and Slide Box listed above are on the "public" side of PNWU's server.
Because we're starting to use the system in the labs in our Histology course, the Slide Box contains a lot of older slides (mainly from the VMD & University of Michigan database; see the "About" menu => "About the slides in Slide Box ..."). To get the list of multifocal-plane slides, in SlideBox, use the "Limit by: Number of focal planes" criterion (on the left side of the 1
st page of Slide Box; select "multiple focal planes" and then click the "Get list of slides" button). Similarly, all of the slides that I've scanned at PNWU are at a maximum magnification of 14.4 pixels/µm, (which is a nominal resolution of ~140nm); to get a list of these slides, use SlideBox's "Limit by: Source" criterion (select the "PNWU" option from the drop-down menu, and then click "Get list of slides" button). I'm still in the process of writing the instruction manual for the Viewer (there are a pair of short instructions regarding navigating the slide on the Viewer's "About" menu); you can create links to specific slides with the URL:
http://viewer.pnwu.edu?xxx or
http://viewer.pnwu.edu?slide=xxx where "xxx" is the slide number.
This project was "presented" at last year's EB meeting (Rhodes JA, Smircich RPJ, DeVore J (2020) "A High‐Resolution Multifocal‐Plane Virtual Microscope for Teaching Histology" FASEB J. 34(Suppl1):
https://faseb.onlinelibrary.wiley.com/doi/10.1096/fasebj.2020.34.s1.01941), and the poster from that meeting can be seen at:
http://viewer.pnwu.edu/docs/poster_EB2020.pdf. In anticipation of building our own system, when I moved to PNWU we adopted NYU's viewer which uses the Google Maps API (Triola MM, Holloway WJ (2011) "
Enhanced virtual microscopy for collaborative education."
BMC Med.Educ. 11:4.
https://bmcmededuc.biomedcentral.com/articles/10.1186/1472-6920-11-4). It is relatively straight-forward to use the libvips library (
https://libvips.github.io/libvips/API/current/: openslideload() & dzsave()) to convert slides from the *.svs or *.cws format into the 2
x-pyramidal tile-architecture ("Google-Maps format") that is used by our new PNWU viewer and by the older NYU viewer. (e.g., Ettarh R
et al. (2015) "
Construction and Implementation of Multiplatform Virtual Microscopy for Histology" FASEB J. 29(Suppl1):
https://faseb.onlinelibrary.wiley.com/doi/10.1096/fasebj.29.1_supplement.546.4). The NYU viewer software is still available; Google Maps has changed and I now would be hesitant to recommend using Google-Maps-API-dependent software, but let me know if you decide to use the NYU software and need help tracking down a copy.
Hope this is helpful. Hopefully, the Drexel software will work like a charm and you won't have to consider other options.
- - Jim Rhodes
------------------------------
James Rhodes
Pacific Northwest University of Health Sciences
Yakima WA
509-249-7738
------------------------------
Original Message:
Sent: 11-06-2020 10:54
From: Haviva Goldman
Subject: Aperio/Leica and .svs images
Hello,
We developed our own in-house viewer with annotations utilzing zoomify. Uses html not flash and students access slides through weblink. Happy to tell you more.
Haviva
Haviva M. Goldman, Ph.D.
Professor and Vice Chair for Medical Education
Department of Neurobiology and Anatomy
Co-Course Director Molecules to Organs
Co-Course Director Human Structure and Function I
Microanatomy Thread Director
Drexel University
College of Medicine
215-991-8467
hgoldman@drexel.edu