off-topic: microscope slide scanners "I wished I had known..."

[Cromey, Douglas W - (dcromey)]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Since microscope slide scanners were a topic of discussion on the list a little a short time ago, I wonder if those of you who have one would share some of the things that (in hindsight) you wished you had known or considered when you added one (or walked into a core that had one) to your core?

We are considering a combination brightfield and fluorescence slide scanner. There are several to choose from, but I'm not necessarily looking for specific model/vendor recommendations.

For those who might be interested, there's a nice review entitled "A Practical Guide to Whole Slide Imaging: A white paper from the Digital Pathology Association" (2019) DOI: 10.5858/arpa.2018-0343-RA

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator
Dept. of Cellular & Molecular Medicine, University of Arizona
Life Sciences North, Room 463
1333 N. Martin Ave, Tucson, AZ  85721 USA

office:  LSN 463        email: [hidden email]<mailto:[hidden email]>
voice:  520-626-2824       fax:  [phone]

http://swehsc.pharmacy.arizona.edu/micro
Home of: "Microscopy and Imaging Resources on the WWW"

UA Microscopy Alliance - http://microscopy.arizona.edu/

[Csúcs Gábor-3]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Doug,

One advice I can give (based on our experience) is related to the file format. Make sure that the files created in various measurement configurations can be really opened  by your specific analysis software. And here you can't trust the companies, you should really check for yourself. If they offer a "file conversion tool", test this carefully. As illustration I can take an already mentioned example: The scanners from 3D Histech are fast and produced nice images, but the file format is "problematic". They offer a conversion tool but in fluorescence mode this works only for 3 channels. If you want to have 4 channels (or more) it will not work. And the native file format works only with a very few software....

Greetings Gabor




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cromey, Douglas W - (dcromey)
Sent: Thursday, 21 November 2019 00:23
To: [hidden email]
Subject: off-topic: microscope slide scanners "I wished I had known..."

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Since microscope slide scanners were a topic of discussion on the list a little a short time ago, I wonder if those of you who have one would share some of the things that (in hindsight) you wished you had known or considered when you added one (or walked into a core that had one) to your core?

We are considering a combination brightfield and fluorescence slide scanner. There are several to choose from, but I'm not necessarily looking for specific model/vendor recommendations.

For those who might be interested, there's a nice review entitled "A Practical Guide to Whole Slide Imaging: A white paper from the Digital Pathology Association" (2019) DOI: 10.5858/arpa.2018-0343-RA

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator Dept. of Cellular & Molecular Medicine, University of Arizona Life Sciences North, Room 463
1333 N. Martin Ave, Tucson, AZ  85721 USA

office:  LSN 463        email: [hidden email]<mailto:[hidden email]>
voice:  520-626-2824       fax:  [phone]

http://swehsc.pharmacy.arizona.edu/micro
Home of: "Microscopy and Imaging Resources on the WWW"

UA Microscopy Alliance - http://microscopy.arizona.edu/

[Jonkman, James]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi, Doug.  Thanks for the review paper.  We scan nearly 20,000 slides/year through our Aperio brightfield slide scanner, and are up to a thousand or so per year with fluorescence on a Zeiss AxioScan.  When we were replacing our older Aperio (~3 years ago) we considered getting a single scanner that can do both brightfield and fluorescence.  However, since fluorescence is MUCH more time consuming we decided to get 2 new scanners instead so that fluorescence jobs don't tie up the scanner and delay brightfield scanning.  The Aperio AT2 with 400 slide loader gives us excellent throughput for brightfield scanning, while our Zeiss AxioScan works well for fluorescence (it can do brightfield too).  So I guess my first suggestion would be if you are in a research hospital like me and have lots of brightfield slides, consider having a dedicated brightfield scanner and then a second scanner for everything else.

Note, our slide scanners are used by my staff only - we don't train users to run them.  This improves throughput and, with thousands of slides of expertise we get excellent results nearly every time.  They also watch for overhanging coverslips, uncured mounting media, etc and therefore prevent costly downtime.  I know others allow users to scan themselves, but it hasn't been our approach.

Brightfield is relatively straightforward and we didn't see a huge distinction between the scanners that are out there, particularly if you're looking for one with a more moderate 100-slide loader.  Resolution, speed, quality are all pretty similar.  Line scanning versus camera based scanners doesn't seem to make a big difference (despite what the companies will tell you on both sides of the debate).  Personally, I prefer a scanner that shows me a preview of the tissue, the region it plans to scan (based on tissue finding algorithm), and a map of focus locations.  We scan only research slides (not clinical), and many research slides are pretty ugly.  If we allowed the automatic tissue finding and focus algorithms to run, our failure rate would be probably 10 to 20%.  On the other hand, after running the preview on a batch of slides, our operators (my staff) review them and adjust the tissue area and focus points to exclude junk and this lowers the failure rate below 1%.  By failure rate, I mean that if there is a focal point on a piece of junk on the slide, then you will have a region that will be out of focus.  Ironically, clinicians wouldn't care, since they could still make their diagnosis; but students seem to care a great deal when the scan isn't absolutely perfect.

As for fluorescence, one thing I found out pretty quickly when demoing scanners 3 or 4 years ago was that many people use non-hardening mountants for fluorescence.  Some scanners (3D Histech for example) have the slides vertical in the racks, and overnight the coverslips slipped (you risk goo-ing up the innards).  Horizontal mounting of slides may be crucial - it's hard to get your customers to change their specimen prep habits (and I believe the non-hardening mountants are better for many fluorescence tissue applications).  That narrows the field considerably.

The most challenging part of fluorescence slide scanning for us is finding the tissue.  This is one weakness of the Zeiss system.  It's important to outline the tissue very accurately so that there are not empty frames around the tissue - fluorescence slide scanning is slow so empty frames waste time, but more importantly they can affect stitching for regions of the slide.   Zeiss likes to show off their algorithm that lets you outline the tissue on the glass with a sharpie, but this hasn't worked for us since the tissue is nearly invisible (if they have properly matched the RI with the mounting media) and you just can't do it accurately enough.  We then installed a 2.5x objective for a prescan with RAC contrast which in principle should work, but there have been some bugs with that.  So we are left with cranking up the contrast on a brightfield macro camera image and guessing for the region.  I think a proper means for finding the tissue is crucial for fluorescence.  I would love to hear what other users' experience has been in this regard.

When you demo slide scanners, don't fall prey to the "in the interest of time" ploy. It is MUCH easier to scan a small region in the middle of a piece of tissue, compared to entire slides where you have to deal with how well the tissue finder works, focus, stitching.  I suggest setting up some slides to run over lunch and come back and see how it did.

Good luck!
Cheers,
James

----------------------------------------------
   James Jonkman, Staff Scientist
   Advanced Optical Microscopy Facility (AOMF)
   and Wright Cell Imaging Facility (WCIF)
   University Health Network
   MaRS, PMCRT tower, 101 College St., Room 15-305
   Toronto, ON, CANADA    M5G 1L7
  [hidden email]  Tel: [phone]
   www.aomf.ca



-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Cromey, Douglas W - (dcromey)
Sent: Thursday, November 21, 2019 12:23 AM
To: [hidden email]
Subject: off-topic: microscope slide scanners "I wished I had known..."

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Since microscope slide scanners were a topic of discussion on the list a little a short time ago, I wonder if those of you who have one would share some of the things that (in hindsight) you wished you had known or considered when you added one (or walked into a core that had one) to your core?

We are considering a combination brightfield and fluorescence slide scanner. There are several to choose from, but I'm not necessarily looking for specific model/vendor recommendations.

For those who might be interested, there's a nice review entitled "A Practical Guide to Whole Slide Imaging: A white paper from the Digital Pathology Association" (2019) DOI: 10.5858/arpa.2018-0343-RA

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator Dept. of Cellular & Molecular Medicine, University of Arizona Life Sciences North, Room 463
1333 N. Martin Ave, Tucson, AZ  85721 USA

office:  LSN 463        email: [hidden email]<mailto:[hidden email]>
voice:  520-626-2824       fax:  [phone]

http://swehsc.pharmacy.arizona.edu/micro
Home of: "Microscopy and Imaging Resources on the WWW"

UA Microscopy Alliance - http://microscopy.arizona.edu/


This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.

[Denise Ramirez]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi All -

We have two slide scanners in our core (Hamamatsu Nanozoomer and Zeiss Axioscan), which are heavily used (many times nearly 24/7), and I have demo'd a number of other systems.

My favorite system hands down is the Nanozoomer. In terms of image quality, scan speed and ease of use I believe it is the clear winner among the field (at least for brightfield scanning). I have trained hundreds of people on both our systems and while I could fully train someone to use the Nanozoomer for basic brightfield use in probably less than 15 minutes, it takes a full hour or more as well as significant "assisted use/retraining" time commitments for the Axioscan for each new user. Now, some of that is because we predominantly dedicate our Nanozoomer for brightfield and the Axioscan for fluorescence (though they can technically each do both modes) but a lot of it is because of the complexity of setting up the slides in Zen and issues with locating/specifying tissue sections, etc as has been mentioned. Also, our Nanozoomer is going on 10 (!) years old and still going strong. I have word from Hamamatsu reps that the original Nanozoomers are still in the field (~15 yrs old). It's a good sturdy design, and as long as you don't have "abnormal" slides (broken, coverslips hanging off, or God forbid wet mounted) it does what it is supposed to with very few issues. I cannot say the same for the Axioscan (not maintaining the service contract is out of the question as I have to call for service/part replacement issues probably quarterly).

Best,
Denise

Denise M. Ramirez, Ph.D.
Core Manager, Whole Brain Microscopy Facility
Assistant Professor, Dept. of Neurology and Neurotherapeutics
UT Southwestern Medical Center
Dallas, TX 75390-8813
214.648.0203

[Michael Abanto]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

We have a Nikon Ni connected to a Prior slide loader, with rgb and cmos cams for BF/FL, and there’s a Crest spinning disc . We use nikon's JOBS for scanning and are happy with it.
We are now demoing an s60 nano zoom with our histology facility, for more basic applications.

Happy with he Nikon - mainly because of the flexibility/power from JOBS - but it took some time to get it stable and requires staff time for programming JOBS. s60 requires less staff time, is more user friendly and seems nice - but is of course more limited than the nikon.

I’d consider the following before purchasing:
installation time - I know many cases that took months, while others plug and play.
users need/application. Great if you have users independently scanning low or one mag on an easy to use scanner, but will it cover all the applications? if you get something more flexible(complicated)/open, do you have the staff time to handle it? will you in 5 years?
complexity vs usability.
camera. you can’t always choose the latest/best for boxed systems.
objectives. how many do you need and which ones. immersion?
slide corners - how much is lost by slide holder and can you live with it.
Loading mechanism. make sure it works well for your users slides by running soak toast overnight with your users (very imperfect) slides.
slide prep. this is a common source of failure for grabbing/placing robots. does your user slide prep work with your robot. are you labeling with a  sticker (affects robot grabbing).
barcoding/reading.
ease of file naming/modifying/storing/sharing/analysis deployment.
robot fail safes. will the robot stop when it breaks something. when/how.
how your files will work with your analysis software. You might even consider picking the analysis software first and working backwards. note Qupath/Orbit/ilastik etc work pretty well and are open source. but I have not yet found the one (commercial or open) to rule them all.
HSI (or other) color space. remarkably useful for tissue detection and post segmentation of rgb images.
Programmability. hard to beat JOBS.
how will you move/open and store the (large) data.
stitching. on the fly/gpu? is it prone to error. can you keep unstitched data and stitch it later?
fileformat. is it pyramidal. is it compressed. does it work seemlessly with your analysis software?
what processing and analysis is built in - do you need another software for analysis, or not.

Things you can quantify at demo or get from another customer: failure rate of loading, failure of autofocus, failure of robotics (crashes), service competence. processing/analysis pipeline success.

I agree with file format and i’ve cleaned quite some mounting media our of the hotels. I’d also agree with testing as many whole slide applications, using as many slides (dusty, gooey and overhanging glass) as you can.

> On Nov 21, 2019, at 1:20 PM, Csucs Gabor <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear Doug,
>
> One advice I can give (based on our experience) is related to the file format. Make sure that the files created in various measurement configurations can be really opened  by your specific analysis software. And here you can't trust the companies, you should really check for yourself. If they offer a "file conversion tool", test this carefully. As illustration I can take an already mentioned example: The scanners from 3D Histech are fast and produced nice images, but the file format is "problematic". They offer a conversion tool but in fluorescence mode this works only for 3 channels. If you want to have 4 channels (or more) it will not work. And the native file format works only with a very few software....
>
> Greetings Gabor
>
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cromey, Douglas W - (dcromey)
> Sent: Thursday, 21 November 2019 00:23
> To: [hidden email]
> Subject: off-topic: microscope slide scanners "I wished I had known..."
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Since microscope slide scanners were a topic of discussion on the list a little a short time ago, I wonder if those of you who have one would share some of the things that (in hindsight) you wished you had known or considered when you added one (or walked into a core that had one) to your core?
>
> We are considering a combination brightfield and fluorescence slide scanner. There are several to choose from, but I'm not necessarily looking for specific model/vendor recommendations.
>
> For those who might be interested, there's a nice review entitled "A Practical Guide to Whole Slide Imaging: A white paper from the Digital Pathology Association" (2019) DOI: 10.5858/arpa.2018-0343-RA
>
> Doug
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Associate Scientific Investigator Dept. of Cellular & Molecular Medicine, University of Arizona Life Sciences North, Room 463
> 1333 N. Martin Ave, Tucson, AZ  85721 USA
>
> office:  LSN 463        email: [hidden email]<mailto:[hidden email]>
> voice:  520-626-2824       fax:  [phone]
>
> http://swehsc.pharmacy.arizona.edu/micro
> Home of: "Microscopy and Imaging Resources on the WWW"
>
> UA Microscopy Alliance - http://microscopy.arizona.edu/

[Brandi Bickford]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Good evening all,
   I am new to this server list, this topic being forwarded to me by my colleague who is manager of the EM/Confocal core beside us, whom we work closely with. We used to be a part of his core, but we grew way to big to have our attention split. I tend to be blunt, tactless, and sarcastic, however i have promised to try my best at professional. So, I apologize upfront if I am make any faux pas.

    We are a hospital core, providing services to clinical faculty, researchers, students, forensics, medico-legal, and outside contractors and institutions. We also run IAS analysis for research and are a beta site for clinical AI.

    If you just want the short version of my opinion:  we have a Hummer, get you and a lot of gear there very reliably, take it across the desert no prob, our Hamamatsu. We also have a Ferrari, can do lots of special things really well, needs an experienced driver, no one else in its class, our Olympus. And at the moment, the Pink Cadillac, the 3-D P1000, lots of room, major large, actually it is more like a G6, just too far to drive. it will make it on time. We demo'd an Aperio, I have and continue to compare that to a used Volkswagon, a really OLD one. Sorry Aperio, I said that I am bluntly honest.

   The longer version: You really have to ask yourself honestly what you are going to use it for, how often, and you should be able to project those needs 5-10 years into the future. Don't buy what you don't need or will not use. that would be all of those extra buttons in my car that keep costing major bucks that I really don't need, I mean a refrigerator in my car? Use that analogy, are those 4 extra channels something you will use? or do you not know what a quantum dot is, or at least not well enough to explain it to a 6 year old, so why do you need to read one?. On this I recommend not asking people, we will all have our opinion which is based on how well we matched. I recommend asking a consulting firm, they handle more than one line, though they may actually rep a few of their favorites, if you hire them to consult, then they will honestly help you to identify your needs and match you to the correct product and the best rep for that product. We use DJTSolutions out of Miami and are extremely pleased with Domenic there. they can also help you to look at what histology equipment you really should have in place to use that scanner. I love one stop shopping, I am way to busy to talk to 6 people about one scanner need, though he hated it when I compared him to EBay, one stop shopping, you get the idea. Whomever you choose is fine, as long as you know them to be experienced and knowledgeable, and trust them, I like to actually enjoy talking to them as well.

   Hamamatsu is a work horse who rarely ever breaks down. Have never had anyone not love the software, very user friendly. Good for research, low mag and low resolution, teaching sets, research master sets, easy surgicals. FL is the only LR scanner I would use for FL. Some of our users submit these as publication images with no prob. One of the first to have 210 capacity loader.

   Olympus is in a class by it's self. Until recently the only scanner that I ever thought should be approved for preliminary diagnosis. Does Cyto and hem, high refractive index and fragile tissue samples without issue. FL is perfect. Polarized perfect. Overlays awesome. TMA module wonderful.  It is just something I don't think we could do without unless we ever said no we can't do that to our clients. Should be used by experienced microscopists only and not multiple users. It is very sophisticated and you shouldn't purchase anything that you don't understand. What is really great here, is that you can add on if your needs change. Warning! A lot of scanners do not permit that, if you need FL now or another channel, sorry, buy an entirely new scanner. Olympus responds immediately to changing needs, just love this company! they are really amiable and fun people. Great people, great product.

P1000, 3-D Histotech, Epredia: It is no longer thermo-fischer, or 3-D, it is Epredia.  Comes very close to the incredible quality of an Olympus, but it is like a Lear jet. It can actually do Cyto's diagnostic quality in about 1 minute per slide. We scanned 1,000 slides last nite, and doing that again tonite. This is what is meant by high thru-put. I am happily amazed and pleased. the thing about this one is that if you know what you are doing you can set your profiles, and if not they can write them for you. Whichever way you go, then the loading and running is not experience required like Olympus but simple. It has bells and whistles, i can't speak to those. I was highly specific about wanting 40X true objective, diagnostic, high-thru-put. And they heard me and gave me exactly that. I like that in a company.

We are running clinicals and research and medico-legals and teaching sets. So we have specific scanners in house or coming in for highly specific needs and don't cross-over unless they need to. We are of course in communication with an FDA approved for preliminary group. Probably not the Volkswagon, of course. But, learn the difference between pleniary, primary, and secondary, to see if you really need that. That is for going totally digital.

We are also looking at Streamers, we have chosen Motic as soon as we are poised to implement. that might be another topic?

thanks for letting me take up your time. We are happy to answer any specific questions.

Brandi