Automatic focus
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Confocal not matter. I am looking for a microscope that can do focus on slides with bacteria without any intervention. I would like to use a XY plate with 8 slides, objectiv 40X dry. Does anyone have an idea? I try IR automatic focus ( Leica, Nikon, Zeiss) but anyone works correctly. thank you |
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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 there, We image live bacteria with a Leica AF6500 system, fully motorized, under the control of the LasAF 3.1.0 software. The built in autofocus algorithm works beautifully for E. coli using a 100x objective and phase contrast (which allows for autofocusing every position and every time point with minimal photodamage). All you need is a good control of the mechanical and thermal drift to be bale to set the appropriate autofocus range. I assume that autofocus with the 40x lense would be less demanding (we really need to go a a speciffic subcellular plane using the 100x), and therefore would work, but it would need to be tryed out. Cheers, Elena ps. IR autofocus references to the coverslip, so it may not be the best strategy for live bacteria unless you use microfluidics... On 7 March 2013 09:32, Pascal Weber <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Confocal not matter. > > I am looking for a microscope that can do focus on slides with bacteria > without > any intervention. I would like to use a XY plate with 8 slides, objectiv > 40X dry. > Does anyone have an idea? I try IR automatic focus ( Leica, Nikon, Zeiss) > but > anyone works correctly. thank you > -- Elena Rebollo Ph.D. --------------------------------------------------------------------------------- Advanced Fluorescence Microscopy Unit IBMB-PCB *http://bit.ly/AfmuBcn *------------------------------------------------------------------------ --------- Molecular Biology Institute of Barcelona (CSIC) C/ Baldiri Reixac, 15-20, 08028 Barcelona (Spain) --------------------------------------------------------------------------------- Tel (+34) 620938111/ (+34) 934020249 --------------------------------------------------------------------------------- <http://www.ibmb.csic.es/index.php?pg=laboratorio&tab=lab_home&idLaboratorio=27> |
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In reply to this post by Pascal Weber
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** For your purpose, these IR systems which simply maintain the coverslip at a fixed distance from the objective are not what you need, and they were never intended for that purpose. What you need is an image analysis system which will search for and find focus (just as a compact digital camera will). I know that SIS (now owned by Olympus) will do this, and I'm sure that most other commercial systems will. There may even be some free systems out there. Guy -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Pascal Weber Sent: Thursday, 7 March 2013 7:33 PM To: [hidden email] Subject: Automatic focus ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Confocal not matter. I am looking for a microscope that can do focus on slides with bacteria without any intervention. I would like to use a XY plate with 8 slides, objectiv 40X dry. Does anyone have an idea? I try IR automatic focus ( Leica, Nikon, Zeiss) but anyone works correctly. thank you |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** there is supposedly a software autofocus in micro-manager ( www.micro-manager.org), but I haven't had reason to use it myself yet these algorithms, and there is more than one, will try to find the plane with the best contrast (=best focus(?)) but if the one above is not good enough, you can add you own algorithm /Johan On Thu, Mar 7, 2013 at 1:23 PM, Guy Cox <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > For your purpose, these IR systems which simply maintain the coverslip at > a fixed distance from the objective are not what you need, and they were > never intended for that purpose. What you need is an image analysis system > which will search for and find focus (just as a compact digital camera > will). I know that SIS (now owned by Olympus) will do this, and I'm sure > that most other commercial systems will. There may even be some free > systems out there. > > Guy > > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] > On Behalf Of Pascal Weber > Sent: Thursday, 7 March 2013 7:33 PM > To: [hidden email] > Subject: Automatic focus > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Confocal not matter. > > I am looking for a microscope that can do focus on slides with bacteria > without > any intervention. I would like to use a XY plate with 8 slides, objectiv > 40X dry. > Does anyone have an idea? I try IR automatic focus ( Leica, Nikon, Zeiss) > but > anyone works correctly. thank you > -- -- ----------------------------------------------------------- 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 Guy Cox-2
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hello Pascal, This is semi commercial response - used to work for Media Cybernetics from 2001-2007, but no longer work for them. The Image-Pro Plus plugin called AFA is specifically designed to tackle problems like the one you describe. As Guy suggests what you are looking for is a contrast based autofocus (not as fast as IR/Laser methods, but more reliable for anything but thing layers of cells adhered directly to the coverslip. Chris Tully Microscopy and Image Analysis Expert [hidden email] 240-475-9753 (c) [image: View my profile on LinkedIn]<http://www.linkedin.com/in/christully/> On Thu, Mar 7, 2013 at 7:23 AM, Guy Cox <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > For your purpose, these IR systems which simply maintain the coverslip at > a fixed distance from the objective are not what you need, and they were > never intended for that purpose. What you need is an image analysis system > which will search for and find focus (just as a compact digital camera > will). I know that SIS (now owned by Olympus) will do this, and I'm sure > that most other commercial systems will. There may even be some free > systems out there. > > Guy > > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] > On Behalf Of Pascal Weber > Sent: Thursday, 7 March 2013 7:33 PM > To: [hidden email] > Subject: Automatic focus > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Confocal not matter. > > I am looking for a microscope that can do focus on slides with bacteria > without > any intervention. I would like to use a XY plate with 8 slides, objectiv > 40X dry. > Does anyone have an idea? I try IR automatic focus ( Leica, Nikon, Zeiss) > but > anyone works correctly. thank you > |
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In reply to this post by Pascal Weber
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** If you have a way to maintain your bacteria in a defined focal plane (agarose gel pad, matrigel, etc...), then IR autofocus should work just fine for you. If the bacteria are not immobilized, then they'll be moving up and down and I am not sure how an image based autofocus will deal with that... it may not be fast enough, and different bacteria will be in different focal planes, so your image based autofocus may get utterly confused... -- Julio Vazquez, Fred Hutchinson Cancer Research Center Seattle, WA 98109-1024 http://www.fhcrc.org/ == On Mar 7, 2013, at 12:32 AM, Pascal Weber wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Confocal not matter. > > I am looking for a microscope that can do focus on slides with bacteria without > any intervention. I would like to use a XY plate with 8 slides, objectiv 40X dry. > Does anyone have an idea? I try IR automatic focus ( Leica, Nikon, Zeiss) but > anyone works correctly. thank you |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Completely agree - and in addition, unless the bacteria are stained, your setup with a 40x dry lens will not give you much useful information. What sort of information DO you want? On Mar 7, 2013, at 12:33 PM, Julio Vazquez wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > If you have a way to maintain your bacteria in a defined focal plane > (agarose gel pad, matrigel, etc...), then IR autofocus should work > just fine for you. If the bacteria are not immobilized, then they'll > be moving up and down and I am not sure how an image based autofocus > will deal with that... it may not be fast enough, and different > bacteria will be in different focal planes, so your image based > autofocus may get utterly confused... > -- > Julio Vazquez, > Fred Hutchinson Cancer Research Center > Seattle, WA 98109-1024 > > > http://www.fhcrc.org/ > > == > > > On Mar 7, 2013, at 12:32 AM, Pascal Weber wrote: > >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> ***** >> >> Confocal not matter. >> >> I am looking for a microscope that can do focus on slides with >> bacteria without >> any intervention. I would like to use a XY plate with 8 slides, >> objectiv 40X dry. >> Does anyone have an idea? I try IR automatic focus ( Leica, Nikon, >> Zeiss) but >> anyone works correctly. thank you Robert J. Palmer Jr., Ph.D. Microbial Receptors Section Laboratory of Cell and Developmental Biology Natl Inst Dental Craniofacial Res - Natl Insts Health Bldg 30, Room 207 30 Convent Drive Bethesda MD 20892 ph 301-594-0025 fax 301-402-0396 |
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In reply to this post by Pascal Weber
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** My problem is: The diagnostic Turberculosis. For this, the system must be able to fully motorized and several blades without human intervention. For this I have four well slide where I do 40 fields at 40X dry, automatically detect bacteria, transferring data in Excel and tell me if the blade is positive or negative. I ran in a first time focus and retain, or regain, when the microscope slide changes. Thank you very much for these first answers. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** What is your sample? Biopsy? Some sort of culture? How do you know the things you are looking at are Mycobacteria? FISH? Antibody? Is this a standard diagnostic technique that you are trying to automate - if so, you can disregard my questions. On Mar 8, 2013, at 1:53 AM, Pascal Weber wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > My problem is: > The diagnostic Turberculosis. For this, the system must be able to > fully motorized > and several blades without human intervention. > For this I have four well slide where I do 40 fields at 40X dry, > automatically > detect bacteria, transferring data in Excel and tell me if the blade > is positive or > negative. I ran in a first time focus and retain, or regain, when > the microscope > slide changes. > Thank you very much for these first answers. Robert J. Palmer Jr., Ph.D. Microbial Receptors Section Laboratory of Cell and Developmental Biology Natl Inst Dental Craniofacial Res - Natl Insts Health Bldg 30, Room 207 30 Convent Drive Bethesda MD 20892 ph 301-594-0025 fax 301-402-0396 |
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In reply to this post by Pascal Weber
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** You may want to have a look at some of the digital pathology systems out there. We have one from an Austrain company (Tissuegnostics; Google them if you want to see their products), but many other vendors (Zeiss, Leica, etc..) offer similar products. The system is designed to scan slides (our stage can take eight, but there are automated systems for high throughput). System will autofocus, find objects (assuming good samples) and image them. Typicaly, these are used to scan tissue sections, but we have done smears, TMA slides, etc.... System cam be used in fluorescence or brightfield mode. Some systems are designed for routine scanning and digitization of slides; ours is more flexible in teh sense we can use any fluorescence filter, objective, etc, to suit our needs. This company has some videos on thier web site. Most of this stuff can be done with a standard Research microscope, using laser autofocus, image-based autofocus, or a combination of both, and the multi-location/tiling capabilities of most current acquisition software. Digital Pathology systems are just optimized for this kind of stuff. Maybe you can get a couple of vendors to run a demo for you. -- Julio Vazquez Fred Hutchinson Cancer Research Center Seattle, WA 98109-1024 http://www.fhcrc.org == On Mar 7, 2013, at 10:53 PM, Pascal Weber wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > My problem is: > The diagnostic Turberculosis. For this, the system must be able to fully motorized > and several blades without human intervention. > For this I have four well slide where I do 40 fields at 40X dry, automatically > detect bacteria, transferring data in Excel and tell me if the blade is positive or > negative. I ran in a first time focus and retain, or regain, when the microscope > slide changes. > Thank you very much for these first answers. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** **** Semi Commercial Reply **** I used to work for Aperio (nearly 1000 of the Digital Pathology Association's estimated 1500 - 2000 installations world wide), but was laid off in Dec 2012 as part of their on going merger with Leica Biosystems. Given the nature of slide scanning these systems are great for large areas but not for time lapse and not for live or even unfixed specimens. When it comes to bacteria, you also need to be careful to do a live evaluation of the system on offer - can you see what you need to see in the images it produces. I never tried to scan a bacterial smear on an Aperio ScanScope, but I was asked to scan some slides of gut tissue stained for H. pilori, and even at 40x (the maximum resolution of the system being evaluated) the details that the pathologists were looking for were not there - this was no surprise though because they could not have seen those details on a standard microscope even with 40x oil. By contrast, I always had very good results scanning CytoSpin slides. My advise is to scan _YOUR_ slides on every scanner you are considering and pick the one that gives the best image. Feel free to contact me through this list, through my personal email ( [hidden email]) or through my new consulting company (Image Incyte, LLC) at [hidden email] for further discussion. Chris Tully Microscopy and Image Analysis Expert [hidden email] 240-475-9753 (c) [image: View my profile on LinkedIn]<http://www.linkedin.com/in/christully/> On Fri, Mar 8, 2013 at 12:07 PM, Julio Vazquez <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > You may want to have a look at some of the digital pathology systems out > there. We have one from an Austrain company (Tissuegnostics; Google them if > you want to see their products), but many other vendors (Zeiss, Leica, > etc..) offer similar products. The system is designed to scan slides (our > stage can take eight, but there are automated systems for high throughput). > System will autofocus, find objects (assuming good samples) and image them. > Typicaly, these are used to scan tissue sections, but we have done smears, > TMA slides, etc.... System cam be used in fluorescence or brightfield > mode. Some systems are designed for routine scanning and digitization of > slides; ours is more flexible in teh sense we can use any fluorescence > filter, objective, etc, to suit our needs. This company has some videos on > thier web site. Most of this stuff can be done with a standard Research > microscope, using laser autofocus, image-based autofocus, or a combination > of both, and the multi-location/tiling capabilities of most current > acquisition software. Digital Pathology systems are just optimized for this > kind of stuff. Maybe you can get a couple of vendors to run a demo for you. > -- > Julio Vazquez > Fred Hutchinson Cancer Research Center > Seattle, WA 98109-1024 > > > http://www.fhcrc.org > > == > > > On Mar 7, 2013, at 10:53 PM, Pascal Weber wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > ***** > > > > My problem is: > > The diagnostic Turberculosis. For this, the system must be able to fully > motorized > > and several blades without human intervention. > > For this I have four well slide where I do 40 fields at 40X dry, > automatically > > detect bacteria, transferring data in Excel and tell me if the blade is > positive or > > negative. I ran in a first time focus and retain, or regain, when the > microscope > > slide changes. > > Thank you very much for these first answers. > |
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