Slide scanner
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? Thank-you sue |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi Sue, Our experience with the Leica scanner was not too good. We rented one for a month to scan a number of slides and try the instrument out, but were very disappointed as it appeared to have a number of problems. It often shut down during a run and the software was not very user friendly. Also, we couldn't read the image files, as we were assured we would be able to until the company created a translator for us. We have two Olympus Nanozoomers in our building and have found they are much better. We've also tried out the Aperio system, but I think that company requires a monthly fee to use their instrument even after it has been purchased. Another scanner you might consider is the Olympus VS120. We have tried that one out as well and the new model is much superior to the old model which was very slow. Good luck, Doug Bray -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Sue Penrhyn-Lowe Sent: Monday, March 25, 2013 10:33 AM To: [hidden email] Subject: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? Thank-you sue |
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In reply to this post by Sue Penrhyn-Lowe
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** We have an Olympus VS120 in one of our facilities. It works fairly well, but the post-acquisition software, OlyVIA, is pretty horrible. We've had trouble just using it for simple things like annotation. If you can get the files into ImageJ or other preferred analysis software it would be a very good system for acquisition. Craig On Mon, Mar 25, 2013 at 10:33 AM, Sue Penrhyn-Lowe <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and > bright field capabilities. What are your thoughts on the leica SCN400F? > Thank-you > sue > |
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In reply to this post by Sue Penrhyn-Lowe
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** On Mon, Mar 25, 2013 at 5:33 PM, Sue Penrhyn-Lowe <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and > bright field capabilities. What are your thoughts on the leica SCN400F? > I have only quickly used a bd pathway. Many many options in the user interface, but in my opinion it still did not offer enough flexibility. Plus, the system is slow and the hardware isn't very fancy. I think you pay a lot extra for having a "total solution" as opposed to when you roll your own. So - get any microscope of your choice (bright-field or spinning disk) with an XY-stage and install www.micro-manager.org You get more flexibility and the system will last longer. There are many free stitching programs, some which produce better results than commercial solutions /Johan > Thank-you > sue > -- -- ----------------------------------------------------------- Johan Henriksson, PhD Karolinska Institutet Ecobima AB - Custom solutions for life sciences http://www.ecobima.com http://mahogny.areta.org http://www.endrov.net <http://www.endrov.net> |
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In reply to this post by Sue Penrhyn-Lowe
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** We had a demo of the Huron technologies tissue scope last year. It performed very well and had decent post acquisition software for visualization and annotation. http://huron-technologies.com/index.html No commercial interest. Jim On Mon, Mar 25, 2013 at 11:33 AM, Sue Penrhyn-Lowe <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and > bright field capabilities. What are your thoughts on the leica SCN400F? > Thank-you > sue > |
 
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Romin, Yevgeniy/Sloan Kettering Institute |
Re: Slide scanner
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In reply to this post by Sue Penrhyn-Lowe
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** We've had a positive experience with Zeiss/3d Histech/Perkin Elmer scanners ( I believe that is the progression of the companies those particular scanners fell under during our ownership of them). I would also recommend using another software for analysis after export (Metamorph or ImageJ for example). Yevgeniy ________________________________________ From: Confocal Microscopy List [[hidden email]] On Behalf Of Sue Penrhyn-Lowe [[hidden email]] Sent: Monday, March 25, 2013 12:33 PM To: [hidden email] Subject: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? Thank-you sue ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Heh. The companies always seem to forget that you actually want to do something with the pretty pictures once you've acquired them. Usually the acquisition software is great but good luck if you want to actually do something with it after the fact. I guess they all assume you're going to fork out the money for Metamorph or something. Craig On Mon, Mar 25, 2013 at 1:28 PM, Yevgeniy Romin <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > We've had a positive experience with Zeiss/3d Histech/Perkin Elmer > scanners ( I believe that is the progression of the companies those > particular scanners fell under during our ownership of them). I would also > recommend using another software for analysis after export (Metamorph or > ImageJ for example). > > Yevgeniy > ________________________________________ > From: Confocal Microscopy List [[hidden email]] On > Behalf Of Sue Penrhyn-Lowe [[hidden email]] > Sent: Monday, March 25, 2013 12:33 PM > To: [hidden email] > Subject: Slide scanner > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and > bright field capabilities. What are your thoughts on the leica SCN400F? > Thank-you > sue > > > > ===================================================================== > > Please note that this e-mail and any files transmitted from > Memorial Sloan-Kettering Cancer Center may be privileged, > confidential, > and protected from disclosure under applicable law. If the reader of > this message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, > you are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this > message > and deleting this message, any attachments, and all copies and backups > from your computer. > |
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In reply to this post by Romin, Yevgeniy/Sloan Kettering Institute
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** **Commercial Response** I'm writing from Media Cybernetics, developers of Image-Pro Premier software. Since some folks are mentioning the need for good post-acquisition analysis software, I thought I'd share that Image-Pro Premier software now allows you to open large slide scanning files. It currently open BigTiff, Aperio, Objective Imaging Turboscan files and will soon open Leica slide scanning files. Once the image is opened, you can extract out a portion to analyze with tools like Smart Segmentation, automatic counting & classification, batch processing, Send to PowerPoint, PDF reporting and annotations. Here's some additional information: http://www.mediacy.com/index.aspx?page=Pathology Downloadable 14-day trials are available via our website. http://www.mediacy.com/index.aspx?page=IP_Premier We also have a DAB Analysis App which is freely available to all Image-Pro Premier users. I'm also looking for collaborators to help us develop new Image-Pro Premier Apps, so please email me if you are interested. Thanks, Kathy Kathy Hrach Media Cybernetics, Inc. 401 N. Washington St, Suite 350 Rockville, MD 20850 tel 301-495-3305 ext. 260 mobile 240-372-2010 fax 301-495-5964 email [hidden email] www.mediacy.com ________________________________________ From: Confocal Microscopy List [[hidden email]] On Behalf Of Sue Penrhyn-Lowe [[hidden email]] Sent: Monday, March 25, 2013 12:33 PM To: [hidden email] Subject: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? Thank-you sue ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
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Romin, Yevgeniy/Sloan Kettering Institute |
Re: Slide scanner
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In reply to this post by Craig Brideau
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Well, maybe they think in terms of "Why reinvent the wheel?", since nowadays you can do pretty much any image analysis using programs like ImageJ or MatLab, which aren't expensive and are available to most people.. Yevgeniy ________________________________________ From: Confocal Microscopy List [[hidden email]] On Behalf Of Craig Brideau [[hidden email]] Sent: Monday, March 25, 2013 4:13 PM To: [hidden email] Subject: Re: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Heh. The companies always seem to forget that you actually want to do something with the pretty pictures once you've acquired them. Usually the acquisition software is great but good luck if you want to actually do something with it after the fact. I guess they all assume you're going to fork out the money for Metamorph or something. Craig On Mon, Mar 25, 2013 at 1:28 PM, Yevgeniy Romin <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > We've had a positive experience with Zeiss/3d Histech/Perkin Elmer > scanners ( I believe that is the progression of the companies those > particular scanners fell under during our ownership of them). I would also > recommend using another software for analysis after export (Metamorph or > ImageJ for example). > > Yevgeniy > ________________________________________ > From: Confocal Microscopy List [[hidden email]] On > Behalf Of Sue Penrhyn-Lowe [[hidden email]] > Sent: Monday, March 25, 2013 12:33 PM > To: [hidden email] > Subject: Slide scanner > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and > bright field capabilities. What are your thoughts on the leica SCN400F? > Thank-you > sue > > > > ===================================================================== > > Please note that this e-mail and any files transmitted from > Memorial Sloan-Kettering Cancer Center may be privileged, > confidential, > and protected from disclosure under applicable law. If the reader of > this message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, > you are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this > message > and deleting this message, any attachments, and all copies and backups > from your computer. > |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Oh yes, I agree with what you are saying for analysis, but for instance Olyvia had trouble with just simple annotation and the like. If all I want to do is put an arrow into the image with a couple words attached to it I shouldn't have to resort to Matlab. @:-) Craig On Mon, Mar 25, 2013 at 2:27 PM, Yevgeniy Romin <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Well, maybe they think in terms of "Why reinvent the wheel?", since > nowadays you can do pretty much any image analysis using programs like > ImageJ or MatLab, which aren't expensive and are available to most people.. > > Yevgeniy > ________________________________________ > From: Confocal Microscopy List [[hidden email]] On > Behalf Of Craig Brideau [[hidden email]] > Sent: Monday, March 25, 2013 4:13 PM > To: [hidden email] > Subject: Re: Slide scanner > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Heh. The companies always seem to forget that you actually want to do > something with the pretty pictures once you've acquired them. Usually > the acquisition software is great but good luck if you want to actually do > something with it after the fact. I guess they all assume you're going to > fork out the money for Metamorph or something. > > Craig > > > On Mon, Mar 25, 2013 at 1:28 PM, Yevgeniy Romin <[hidden email]> wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > ***** > > > > We've had a positive experience with Zeiss/3d Histech/Perkin Elmer > > scanners ( I believe that is the progression of the companies those > > particular scanners fell under during our ownership of them). I would > also > > recommend using another software for analysis after export (Metamorph or > > ImageJ for example). > > > > Yevgeniy > > ________________________________________ > > From: Confocal Microscopy List [[hidden email]] On > > Behalf Of Sue Penrhyn-Lowe [[hidden email]] > > Sent: Monday, March 25, 2013 12:33 PM > > To: [hidden email] > > Subject: Slide scanner > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > ***** > > > > I am looking to buy a new virtual slide scanner with both Fluorescent and > > bright field capabilities. What are your thoughts on the leica SCN400F? > > Thank-you > > sue > > > > > > > > > ===================================================================== > > > > Please note that this e-mail and any files transmitted from > > Memorial Sloan-Kettering Cancer Center may be privileged, > > confidential, > > and protected from disclosure under applicable law. If the reader of > > this message is not the intended recipient, or an employee or agent > > responsible for delivering this message to the intended recipient, > > you are hereby notified that any reading, dissemination, > distribution, > > copying, or other use of this communication or any of its > attachments > > is strictly prohibited. If you have received this communication in > > error, please notify the sender immediately by replying to this > > message > > and deleting this message, any attachments, and all copies and > backups > > from your computer. > > > |
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In reply to this post by Sue Penrhyn-Lowe
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I have tested a few of these systems out. We currently have access to an Aperio scanner for brightfield slides and we have custom journals written in metamorph that let us scan 4 slides (multiple tissue sections per slide) on our inverted live cell fluorescence system. In would say the best all in one solution I have tried would be the MetaSystems vSlide. It can do both fluorescence and brigthfield, has excellent software and data handling for large images (it uses some part of Imaris). It also has the ability to add a 880 slide loader if you only want to queue up slides once a week:) The one thing to consider with all these systems is the file format they save in, is it conducive to use on a normal PC system, or do you need a massive scary beast just to open the files? The Aperio (vSlide and other dedicated slide scan systems) usually work fine even opening a very large image on a simple PC. But custom stuff like we get out of our MetaMorph driven solution can bring things to a grinding halt on the wrong system. Cheers Cam Cameron J. Nowell Centre for Dynamic Imaging The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville, Victoria 3052 Australia Phone: +61 3 9345 2871 Mobile: +61422882700 Fax: +61 3 9347 0852 Facility Website LinkedIn Profile -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Sue Penrhyn-Lowe Sent: Tuesday, 26 March 2013 3:33 AM To: [hidden email] Subject: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? Thank-you sue ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ |
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In reply to this post by Hrach, Kathy
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi, We have the VS120S slide scanner from Olympus in our facility and is the same system that Craig was mentioning in his reply. This system is very much liked by users for its simplicity and good quality images. As Craig has mentioned, there are no software to open the .vsi images generated. The stitching is flawless and generates great images. There is an ImageJ VSI reader plugin to open the images (but have been unsuccessful so far to open a large image- but have heard that it has worked fine for at least one user). The OlyVIA software that Craig was mentioning is a freeware and can be used to open the .vsi files and have minimal features like sharing with other users online and taking a snapshot of the screen and export to PPT slides or Photoshop. The drawback is that the resolution of the image will go down when you use OlyVIA software and take a snapshot of the image. The features in the VS-ASW software (which controls the microscope and imaging) is good and user friendly (was able to train users within an hour and they are able to image on their own). The VS-ASW software has many features which are not present in OlyVIA like crop ROI into new image, burn in info (burns the scale bar in the image), annotations, measuring tools, image processing tools (Edge detection, Sharpening tools, smoothing, enhancements, rotation, etc.). The following are the pros and cons of the VS-ASW slide scanner: Pros: -Fast imaging, can scan up to 5 slides in bright field mode and with a slight modification can do the batch scan in fluorescence mode too. The Olympus tech claims that the latest version of the software can do a fluorescence batch scan mode too- but have to see it. -Can do Z-stacks up to 15 microns and EFI processing (Extented Focus Image) in thick sections- good feature for imaging processes like neurons which are in different focal planes -Good quality images with seamless stitching -User friendly software for imaging and hardware control -The hardware (microscope) has not failed on us Cons: -Software crashes too often and has a mind of its own. Has seen it change the settings quite a few times even like disappearance of some features like the batch scan in fluorescence mode, which was an unexplained mystery even to the Olympus techs. -The stand alone Olyvia software has minimal functions and cannot be used for extensive image post-processing - The .vsi file is not compatible with most of the other image processing programs (not sure if Image-Pro can open it and would like to try) -The software is still in infancy and need lots of improvements to make it more stable -Stand alone software (similar to the ones that controls the microscope with all the features) and Upgrades are costly Hope this helps and good luck. Sathya Srinivasan Manager RUN Microscopy Facility www.ucalgary.ca/runcore University of Calgary Calgary, AB, Canada > Date: Mon, 25 Mar 2013 20:20:01 +0000 > From: [hidden email] > Subject: Re: Slide scanner > To: [hidden email] > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > **Commercial Response** > > I'm writing from Media Cybernetics, developers of Image-Pro Premier software. Since some folks are mentioning the need for good post-acquisition analysis software, I thought I'd share that Image-Pro Premier software now allows you to open large slide scanning files. It currently open BigTiff, Aperio, Objective Imaging Turboscan files and will soon open Leica slide scanning files. > > Once the image is opened, you can extract out a portion to analyze with tools like Smart Segmentation, automatic counting & classification, batch processing, Send to PowerPoint, PDF reporting and annotations. Here's some additional information: > http://www.mediacy.com/index.aspx?page=Pathology > > Downloadable 14-day trials are available via our website. http://www.mediacy.com/index.aspx?page=IP_Premier > > We also have a DAB Analysis App which is freely available to all Image-Pro Premier users. I'm also looking for collaborators to help us develop new Image-Pro Premier Apps, so please email me if you are interested. > > Thanks, > Kathy > > > Kathy Hrach > Media Cybernetics, Inc. > 401 N. Washington St, Suite 350 > Rockville, MD 20850 > tel 301-495-3305 ext. 260 > mobile 240-372-2010 > fax 301-495-5964 > email [hidden email] > www.mediacy.com > > > ________________________________________ > From: Confocal Microscopy List [[hidden email]] On Behalf Of Sue Penrhyn-Lowe [[hidden email]] > Sent: Monday, March 25, 2013 12:33 PM > To: [hidden email] > Subject: Slide scanner > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? > Thank-you > sue > > > > ===================================================================== > > Please note that this e-mail and any files transmitted from > Memorial Sloan-Kettering Cancer Center may be privileged, confidential, > and protected from disclosure under applicable law. If the reader of > this message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, > you are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this message > and deleting this message, any attachments, and all copies and backups > from your computer. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi All, We have the MetaSystems VSlide, which we purchased last year. It's microscope-based, i.e. not a box, which is what we wanted so that we have a large range of objective lenses and filter cubes available. It does fluorescence and brightfield. There are 2 cameras, one colour and one monochrome so you can do "high resolution" colour imaging as well using the monochrome camera (3 LEDs are used for the illumination). We tested it out thoroughly prior to purchase and were satisfied that it would be suitable for our requirements. Data can be output in various ways, including Imaris format (.ims) which is hierarchical and can be read in ImageJ/FIJI. Regions can be extracted, etc. using the free MetaViewer. We have been very happy with the performance of the system with only the odd glitch, usually user-related. The main issues we have encountered have been specimen-related since we are a research facility so slides/sections, etc. tend to be quite variable. Also, the file size and requirements for storage have astounded some of our researchers. Let's just say that the 63x/1.4NA oil immersion objective lens isn't getting a lot of use! Kind regards, Jacqui Jacqueline Ross Biomedical Imaging Microscopist Biomedical Imaging Research Unit School of Medical Sciences Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland 1142, NEW ZEALAND Tel: 64 9 923 7438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Sathya Srinivasan Sent: Tuesday, 26 March 2013 10:59 a.m. To: [hidden email] Subject: Re: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi, We have the VS120S slide scanner from Olympus in our facility and is the same system that Craig was mentioning in his reply. This system is very much liked by users for its simplicity and good quality images. As Craig has mentioned, there are no software to open the .vsi images generated. The stitching is flawless and generates great images. There is an ImageJ VSI reader plugin to open the images (but have been unsuccessful so far to open a large image- but have heard that it has worked fine for at least one user). The OlyVIA software that Craig was mentioning is a freeware and can be used to open the .vsi files and have minimal features like sharing with other users online and taking a snapshot of the screen and export to PPT slides or Photoshop. The drawback is that the resolution of the image will go down when you use OlyVIA software and take a snapshot of the image. The features in the VS-ASW software (which controls the microscope and imaging) is good and user friendly (was able to train users within an hour and they are able to image on their own). The VS-ASW software has many features which are not present in OlyVIA like crop ROI into new image, burn in info (burns the scale bar in the image), annotations, measuring tools, image processing tools (Edge detection, Sharpening tools, smoothing, enhancements, rotation, etc.). The following are the pros and cons of the VS-ASW slide scanner: Pros: -Fast imaging, can scan up to 5 slides in bright field mode and with a slight modification can do the batch scan in fluorescence mode too. The Olympus tech claims that the latest version of the software can do a fluorescence batch scan mode too- but have to see it. -Can do Z-stacks up to 15 microns and EFI processing (Extented Focus Image) in thick sections- good feature for imaging processes like neurons which are in different focal planes -Good quality images with seamless stitching -User friendly software for imaging and hardware control -The hardware (microscope) has not failed on us Cons: -Software crashes too often and has a mind of its own. Has seen it change the settings quite a few times even like disappearance of some features like the batch scan in fluorescence mode, which was an unexplained mystery even to the Olympus techs. -The stand alone Olyvia software has minimal functions and cannot be used for extensive image post-processing - The .vsi file is not compatible with most of the other image processing programs (not sure if Image-Pro can open it and would like to try) -The software is still in infancy and need lots of improvements to make it more stable -Stand alone software (similar to the ones that controls the microscope with all the features) and Upgrades are costly Hope this helps and good luck. Sathya Srinivasan Manager RUN Microscopy Facility www.ucalgary.ca/runcore University of Calgary Calgary, AB, Canada > Date: Mon, 25 Mar 2013 20:20:01 +0000 > From: [hidden email] > Subject: Re: Slide scanner > To: [hidden email] > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > **Commercial Response** > > I'm writing from Media Cybernetics, developers of Image-Pro Premier software. Since some folks are mentioning the need for good post-acquisition analysis software, I thought I'd share that Image-Pro Premier software now allows you to open large slide scanning files. It currently open BigTiff, Aperio, Objective Imaging Turboscan files and will soon open Leica slide scanning files. > > Once the image is opened, you can extract out a portion to analyze with tools like Smart Segmentation, automatic counting & classification, batch processing, Send to PowerPoint, PDF reporting and annotations. Here's some additional information: > http://www.mediacy.com/index.aspx?page=Pathology > > Downloadable 14-day trials are available via our website. > http://www.mediacy.com/index.aspx?page=IP_Premier > > We also have a DAB Analysis App which is freely available to all Image-Pro Premier users. I'm also looking for collaborators to help us develop new Image-Pro Premier Apps, so please email me if you are interested. > > Thanks, > Kathy > > > Kathy Hrach > Media Cybernetics, Inc. > 401 N. Washington St, Suite 350 > Rockville, MD 20850 > tel 301-495-3305 ext. 260 > mobile 240-372-2010 > fax 301-495-5964 > email [hidden email] > www.mediacy.com > > > ________________________________________ > From: Confocal Microscopy List [[hidden email]] On > Behalf Of Sue Penrhyn-Lowe [[hidden email]] > Sent: Monday, March 25, 2013 12:33 PM > To: [hidden email] > Subject: Slide scanner > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? > Thank-you > sue > > > > ===================================================================== > > Please note that this e-mail and any files transmitted from Memorial > Sloan-Kettering Cancer Center may be privileged, confidential, and > protected from disclosure under applicable law. If the reader of this > message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, you > are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this > message and deleting this message, any attachments, and all copies and > backups from your computer. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi All, One further comment that I forgot to include in my previous email. We can also do batch imaging, using a slide tower, however in our hands it's really only suitable for brightfield imaging. This is because we have found that it really is necessary to define the exposure time for fluorescence carefully (and manually by going to the brightest region and setting it there) as with a standard fluorescence microscope. Otherwise, it's easy to end up with a load of images that are over-saturated. For fluorescence, you may not have the luxury of being able to repeat the scanning due to photobleaching. Kind regards, Jacqui Jacqueline Ross Biomedical Imaging Microscopist Biomedical Imaging Research Unit School of Medical Sciences Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland 1142, NEW ZEALAND Tel: 64 9 923 7438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Jacqui Ross Sent: Tuesday, 26 March 2013 5:37 p.m. To: [hidden email] Subject: Re: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi All, We have the MetaSystems VSlide, which we purchased last year. It's microscope-based, i.e. not a box, which is what we wanted so that we have a large range of objective lenses and filter cubes available. It does fluorescence and brightfield. There are 2 cameras, one colour and one monochrome so you can do "high resolution" colour imaging as well using the monochrome camera (3 LEDs are used for the illumination). We tested it out thoroughly prior to purchase and were satisfied that it would be suitable for our requirements. Data can be output in various ways, including Imaris format (.ims) which is hierarchical and can be read in ImageJ/FIJI. Regions can be extracted, etc. using the free MetaViewer. We have been very happy with the performance of the system with only the odd glitch, usually user-related. The main issues we have encountered have been specimen-related since we are a research facility so slides/sections, etc. tend to be quite variable. Also, the file size and requirements for storage have astounded some of our researchers. Let's just say that the 63x/1.4NA oil immersion objective lens isn't getting a lot of use! Kind regards, Jacqui Jacqueline Ross Biomedical Imaging Microscopist Biomedical Imaging Research Unit School of Medical Sciences Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland 1142, NEW ZEALAND Tel: 64 9 923 7438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Sathya Srinivasan Sent: Tuesday, 26 March 2013 10:59 a.m. To: [hidden email] Subject: Re: Slide scanner ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi, We have the VS120S slide scanner from Olympus in our facility and is the same system that Craig was mentioning in his reply. This system is very much liked by users for its simplicity and good quality images. As Craig has mentioned, there are no software to open the .vsi images generated. The stitching is flawless and generates great images. There is an ImageJ VSI reader plugin to open the images (but have been unsuccessful so far to open a large image- but have heard that it has worked fine for at least one user). The OlyVIA software that Craig was mentioning is a freeware and can be used to open the .vsi files and have minimal features like sharing with other users online and taking a snapshot of the screen and export to PPT slides or Photoshop. The drawback is that the resolution of the image will go down when you use OlyVIA software and take a snapshot of the image. The features in the VS-ASW software (which controls the microscope and imaging) is good and user friendly (was able to train users within an hour and they are able to image on their own). The VS-ASW software has many features which are not present in OlyVIA like crop ROI into new image, burn in info (burns the scale bar in the image), annotations, measuring tools, image processing tools (Edge detection, Sharpening tools, smoothing, enhancements, rotation, etc.). The following are the pros and cons of the VS-ASW slide scanner: Pros: -Fast imaging, can scan up to 5 slides in bright field mode and with a slight modification can do the batch scan in fluorescence mode too. The Olympus tech claims that the latest version of the software can do a fluorescence batch scan mode too- but have to see it. -Can do Z-stacks up to 15 microns and EFI processing (Extented Focus Image) in thick sections- good feature for imaging processes like neurons which are in different focal planes -Good quality images with seamless stitching -User friendly software for imaging and hardware control -The hardware (microscope) has not failed on us Cons: -Software crashes too often and has a mind of its own. Has seen it change the settings quite a few times even like disappearance of some features like the batch scan in fluorescence mode, which was an unexplained mystery even to the Olympus techs. -The stand alone Olyvia software has minimal functions and cannot be used for extensive image post-processing - The .vsi file is not compatible with most of the other image processing programs (not sure if Image-Pro can open it and would like to try) -The software is still in infancy and need lots of improvements to make it more stable -Stand alone software (similar to the ones that controls the microscope with all the features) and Upgrades are costly Hope this helps and good luck. Sathya Srinivasan Manager RUN Microscopy Facility www.ucalgary.ca/runcore University of Calgary Calgary, AB, Canada > Date: Mon, 25 Mar 2013 20:20:01 +0000 > From: [hidden email] > Subject: Re: Slide scanner > To: [hidden email] > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > **Commercial Response** > > I'm writing from Media Cybernetics, developers of Image-Pro Premier software. Since some folks are mentioning the need for good post-acquisition analysis software, I thought I'd share that Image-Pro Premier software now allows you to open large slide scanning files. It currently open BigTiff, Aperio, Objective Imaging Turboscan files and will soon open Leica slide scanning files. > > Once the image is opened, you can extract out a portion to analyze with tools like Smart Segmentation, automatic counting & classification, batch processing, Send to PowerPoint, PDF reporting and annotations. Here's some additional information: > http://www.mediacy.com/index.aspx?page=Pathology > > Downloadable 14-day trials are available via our website. > http://www.mediacy.com/index.aspx?page=IP_Premier > > We also have a DAB Analysis App which is freely available to all Image-Pro Premier users. I'm also looking for collaborators to help us develop new Image-Pro Premier Apps, so please email me if you are interested. > > Thanks, > Kathy > > > Kathy Hrach > Media Cybernetics, Inc. > 401 N. Washington St, Suite 350 > Rockville, MD 20850 > tel 301-495-3305 ext. 260 > mobile 240-372-2010 > fax 301-495-5964 > email [hidden email] > www.mediacy.com > > > ________________________________________ > From: Confocal Microscopy List [[hidden email]] On > Behalf Of Sue Penrhyn-Lowe [[hidden email]] > Sent: Monday, March 25, 2013 12:33 PM > To: [hidden email] > Subject: Slide scanner > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? > Thank-you > sue > > > > ===================================================================== > > Please note that this e-mail and any files transmitted from Memorial > Sloan-Kettering Cancer Center may be privileged, confidential, and > protected from disclosure under applicable law. If the reader of this > message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, you > are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this > message and deleting this message, any attachments, and all copies and > backups from your computer. |
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In reply to this post by Sue Penrhyn-Lowe
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi Sue we have two system in my lab the 3D-histech Scan which has been operating for five years now and the Lecia scn400 for two years. After the latest upgrade the 3D-Histech system keeps the focus well in both imaging modes, the Leica system also keeps focus well and operates at a reasonable speed. We initally had problems with both systems but now on both the operating software seems solid. The 3D-Histech and Leica free software allows for export of grabs of the data at screen resolution. For analysis we run the software through Definiens Tissue Studio ( http://tissuestudio.definiens.com ) which gave us greater measurement capabilities than the instrument supplied software. You might want to look at the Perkinelmer Vectra ( http://www.perkinelmer.co.uk/Catalog/Category/ID/Vectra ) as spectrophotometric imaging the tissue would allow greater multiplexing in both brightfield and fluorescence mode, and help to remove autofluorescence. We are considering this at the moment as we wish to throw a huge number of labelling regimes onto our TMAs. Hope this helps Steve Steve Bagley Head of Advanced Imaging and Flow Cytometry | Paterson Institute for Cancer Research | Cancer Research UK | University of Manchester | Wilmslow Road | Manchester | UK | M20 4BX | www:http://goo.gl/R828Q On 26 Mar 2013, at 05:07, CONFOCALMICROSCOPY automatic digest system <[hidden email]<mailto:[hidden email]>> wrote: From: Sue Penrhyn-Lowe <[hidden email]<mailto:[hidden email]>> Subject: Slide scanner Date: 25 March 2013 16:33:26 GMT ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I am looking to buy a new virtual slide scanner with both Fluorescent and bright field capabilities. What are your thoughts on the leica SCN400F? Thank-you sue ________________________________ This email is confidential and intended solely for the use of the person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Paterson Institute for Cancer Research or the University of Manchester. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible. |
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In reply to this post by Sue Penrhyn-Lowe
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I visited a lab at USAMRIID in Maryland who had major problems with their Leica SCN4000. This was in January 2012 - hopefully Leica either fixed the problem(s) or gave the customer their money back. I'll apeculate that SCN problem(s) could be one reason Leica(Danaher) purchased Aperio. I recommend demo'ing the Hamamatsu NanoZoomer vs whatever other machines (and sales reps) seem reasonable. Ideally have the demo machine(s) running for at least a week. I recommend scanning at least overnight, and if you are going for a high capacitgy model, overnight or over the weekend. Since you want fluorescence, insist on a solid state illuminator, such as the Lumencor SOLA / SPECTRA X or Lumen Dynamics X-LED or Chroma/89North's equivalent. Any digital slide imaging system vendor still pushing an arc lamp or even metal halide lamp is out of date. best wishes, George -----Original Message----- >From: Sue Penrhyn-Lowe <[hidden email]> >Sent: Mar 25, 2013 11:33 AM >To: [hidden email] >Subject: Slide scanner > >***** >To join, leave or search the confocal microscopy listserv, go to: >http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >***** > >I am looking to buy a new virtual slide scanner with both Fluorescent and >bright field capabilities. What are your thoughts on the leica SCN400F? >Thank-you >sue |
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In reply to this post by Craig Brideau
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I've been using many of these systems lately. I do use the slide scanners in a commercial setting but have no commercial interest in selling them. Some quick thoughts on the systems I see routinely: - Pannoramic Scan. Perkin Elmer. 150 slide loader. I think they have a 250 version now. Fluor/Brightfield. Probably the most complete system from ease of use to robustness and analysis. It is the one we use most. Very flexible. Solid images. I like where they are going with a lot of their stuff too. A clean iPad app, online hosting etc… Reasonably capable free viewer for the mrxs files. - Nanozoomer HT. 210 slide loader. Fluor/Brightfield. They claim '40X' but it is effectively a 2X zoom in front of the camera on the single objective in the system. Not a big deal but you should be aware of the type of image coming off the system. Probably has the best walk-away capability and great flexibility/speed for walk-away acquisition. The analysis I've seen is weak. You'll almost definitely get things analyzed with other software. It has a nice feature for group settings where you can interrupt a large batch of slides to do an independent 2nd batch of slides without losing your progress on the first batch. Great for squeezing in 1 or 2 slides when a batch 200 are already running… Free viewer for the ndpi files. - Aperio probably has the biggest install/user base. These systems work well enough but I wouldn't pick them above either the Nanozoomer or Perkin Elmer systems at this point. They do have a nice free viewer that supports many of the competing formats from their svs to ndpi, mrxs etc. - Huron. I haven't used these systems myself but have seen a fair number of images from their system. The image quality is very nice and they are great for large samples. Scanning an 8 inch x 6 inch slide is amazing if you have the need. Automated whole slide capabilities are being added to more and more standard microscope and HCS systems of course too. Your degree of convenience/scripting/customization will vary with each of course. Best wishes, Casey On Mar 25, 2013, at 10:08 AM, Craig Brideau <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > We have an Olympus VS120 in one of our facilities. It works fairly well, > but the post-acquisition software, OlyVIA, is pretty horrible. We've had > trouble just using it for simple things like annotation. If you can get > the files into ImageJ or other preferred analysis software it would be a > very good system for acquisition. > > Craig > > > On Mon, Mar 25, 2013 at 10:33 AM, Sue Penrhyn-Lowe <[hidden email]> wrote: > >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> ***** >> >> I am looking to buy a new virtual slide scanner with both Fluorescent and >> bright field capabilities. What are your thoughts on the leica SCN400F? >> Thank-you >> sue >> > > |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** How about the Panoptiq system from ViewsIQ? You can use it on your own microscope, it is relatively inexpensive and it works really well!! Check http://viewsiq.ca/ They will do a free webinar so you can see how it works and discuss your particular needs. No harm in looking! Loralei On Thu, Mar 28, 2013 at 10:12 AM, Casey Laris <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I've been using many of these systems lately. I do use the slide scanners > in a commercial setting but have no commercial interest in selling them. > > Some quick thoughts on the systems I see routinely: > > - Pannoramic Scan. Perkin Elmer. 150 slide loader. I think they have a 250 > version now. Fluor/Brightfield. Probably the most complete system from ease > of use to robustness and analysis. It is the one we use most. Very > flexible. Solid images. I like where they are going with a lot of their > stuff too. A clean iPad app, online hosting etc… Reasonably capable free > viewer for the mrxs files. > - Nanozoomer HT. 210 slide loader. Fluor/Brightfield. They claim '40X' but > it is effectively a 2X zoom in front of the camera on the single objective > in the system. Not a big deal but you should be aware of the type of image > coming off the system. Probably has the best walk-away capability and great > flexibility/speed for walk-away acquisition. The analysis I've seen is > weak. You'll almost definitely get things analyzed with other software. It > has a nice feature for group settings where you can interrupt a large batch > of slides to do an independent 2nd batch of slides without losing your > progress on the first batch. Great for squeezing in 1 or 2 slides when a > batch 200 are already running… Free viewer for the ndpi files. > - Aperio probably has the biggest install/user base. These systems work > well enough but I wouldn't pick them above either the Nanozoomer or Perkin > Elmer systems at this point. They do have a nice free viewer that supports > many of the competing formats from their svs to ndpi, mrxs etc. > - Huron. I haven't used these systems myself but have seen a fair number > of images from their system. The image quality is very nice and they are > great for large samples. Scanning an 8 inch x 6 inch slide is amazing if > you have the need. > > Automated whole slide capabilities are being added to more and more > standard microscope and HCS systems of course too. Your degree of > convenience/scripting/customization will vary with each of course. > > Best wishes, > > Casey > > On Mar 25, 2013, at 10:08 AM, Craig Brideau <[hidden email]> > wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > ***** > > > > We have an Olympus VS120 in one of our facilities. It works fairly well, > > but the post-acquisition software, OlyVIA, is pretty horrible. We've had > > trouble just using it for simple things like annotation. If you can get > > the files into ImageJ or other preferred analysis software it would be a > > very good system for acquisition. > > > > Craig > > > > > > On Mon, Mar 25, 2013 at 10:33 AM, Sue Penrhyn-Lowe <[hidden email]> > wrote: > > > >> ***** > >> To join, leave or search the confocal microscopy listserv, go to: > >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >> ***** > >> > >> I am looking to buy a new virtual slide scanner with both Fluorescent > and > >> bright field capabilities. What are your thoughts on the leica SCN400F? > >> Thank-you > >> sue > >> > > > > > |
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