software
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dea all, Does anyone know of software that selects only in focus portions of an image and discards the out-of-focus parts. We need to get clear views of a curved surface (the fly eye) with a 10x objective using reflected light. Only thin optical slices are in focus at this mag, but if we could put together the portions that are in focus over the entire depth of the specimen, we could rebuild a clean image of the structure. This wouild be a used in an assay screening a bizillion flies, so SEM is not really practical. thanks, Carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Carl - NIS-Elements (Nikon's software) has a tool like this - they call it Extended Depth of Focus. I haven't used it very much but this is exactly what it does. Kurt Carl Boswell wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dea all, > Does anyone know of software that selects only in focus portions of an > image and discards the out-of-focus parts. We need to get clear views > of a curved surface (the fly eye) with a 10x objective using reflected > light. Only thin optical slices are in focus at this mag, but if we > could put together the portions that are in focus over the entire > depth of the specimen, we could rebuild a clean image of the > structure. This wouild be a used in an assay screening a bizillion > flies, so SEM is not really practical. > thanks, > Carl > > Carl A. Boswell, Ph.D. > Molecular and Cellular Biology > University of Arizona > 520-954-7053 > FAX 520-621-3709 -- Kurt Thorn, PhD Director, Nikon Imaging Center University of California San Francisco UCSF MC 2140 Genentech Hall Room S252 600 16th St. San Francisco, CA 94158-2517 http://nic.ucsf.edu phone 415.514.9709 fax 415.514.4300 |
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In reply to this post by Boswell, Carl A - (cboswell)
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal MetaMorph's 'Best Focus' projection does this. Steve -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell Sent: Friday, October 05, 2007 7:35 PM To: [hidden email] Subject: software Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dea all, Does anyone know of software that selects only in focus portions of an image and discards the out-of-focus parts. We need to get clear views of a curved surface (the fly eye) with a 10x objective using reflected light. Only thin optical slices are in focus at this mag, but if we could put together the portions that are in focus over the entire depth of the specimen, we could rebuild a clean image of the structure. This wouild be a used in an assay screening a bizillion flies, so SEM is not really practical. thanks, Carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 |
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In reply to this post by Boswell, Carl A - (cboswell)
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Carl, I've used this plugin for ImageJ. It does appear that one loses a few gray levels in the end result, at least with this plugin and a with commercial product to which it was compared. http://rsb.info.nih.gov/ij/plugins/stack-focuser.html Regards, Glen Glen MacDonald Core for Communication Research Virginia Merrill Bloedel Hearing Research Center Box 357923 University of Washington Seattle, WA 98195-7923 USA (206) 616-4156 [hidden email] ************************************************************************ ****** The box said "Requires WindowsXP or better", so I bought a Macintosh. ************************************************************************ ****** On Oct 5, 2007, at 4:34 PM, Carl Boswell wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dea all, > Does anyone know of software that selects only in focus portions of > an image and discards the out-of-focus parts. We need to get clear > views of a curved surface (the fly eye) with a 10x objective using > reflected light. Only thin optical slices are in focus at this > mag, but if we could put together the portions that are in focus > over the entire depth of the specimen, we could rebuild a clean > image of the structure. This wouild be a used in an assay > screening a bizillion flies, so SEM is not really practical. > thanks, > Carl > > Carl A. Boswell, Ph.D. > Molecular and Cellular Biology > University of Arizona > 520-954-7053 > FAX 520-621-3709 |
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In reply to this post by Boswell, Carl A - (cboswell)
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
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Hi Carl, I think that's what the imageJ plugin "Stack Focuser" does. Check it at at the imagej website: I believe Metamorph, and possibly other software packages have similar tools, often called "Extended depth of focus" or similar -- Julio Vazquez Fred Hutchinson Cancer Research Center Seattle, WA 98109-1024 On Oct 5, 2007, at 4:34 PM, Carl Boswell wrote:
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In reply to this post by Boswell, Carl A - (cboswell)
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dera Carl, Most imaging packages have "extended depth of focus" modules in them these days. We use the small (i.e. cheap) version of AutoMontage from Syncroscopy, which does a reasonable job, and the license dongle can be moved between computers. The expensive full version does a very good job but has to remain on one computer, which can be a pain. We've also tried the non-commercial CombineZ - www.hadleyweb.pwp.blueyonder.co.uk/CZM/combinezm.htm, which is good too. cheers, Rosemary Dr Rosemary White [hidden email] CSIRO Plant Industry ph. 61 (0)2-6246 5475 GPO Box 1600 fax. 61 (0)2-6246 5334 Canberra, ACT 2601 Australia > From: Carl Boswell <[hidden email]> > Reply-To: Confocal Microscopy List <[hidden email]> > Date: Fri, 5 Oct 2007 16:34:55 -0700 > To: <[hidden email]> > Subject: software > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dea all, > Does anyone know of software that selects only in focus portions of an image > and discards the out-of-focus parts. We need to get clear views of a curved > surface (the fly eye) with a 10x objective using reflected light. Only thin > optical slices are in focus at this mag, but if we could put together the > portions that are in focus over the entire depth of the specimen, we could > rebuild a clean image of the structure. This wouild be a used in an assay > screening a bizillion flies, so SEM is not really practical. > thanks, > Carl > > Carl A. Boswell, Ph.D. > Molecular and Cellular Biology > University of Arizona > 520-954-7053 > FAX 520-621-3709 |
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In reply to this post by Boswell, Carl A - (cboswell)
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I have been using Helicon Focus for the past year and it works very well. Here is a link with a few examples. http://www.heliconsoft.com/heliconfocus.html Cheers, Michael Michael Weis Electron Microscopy & Digital Imaging Pacific Agri-Food Research Centre Agriculture and Agri-Food Canada 4200 Highway 97 Summerland, BC V0H 1Z0 Telephone: 250-494-6410 Facsimile: 250-494-0755 [hidden email] -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell Sent: Friday, October 05, 2007 4:35 PM To: [hidden email] Subject: software Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dea all, Does anyone know of software that selects only in focus portions of an image and discards the out-of-focus parts. We need to get clear views of a curved surface (the fly eye) with a 10x objective using reflected light. Only thin optical slices are in focus at this mag, but if we could put together the portions that are in focus over the entire depth of the specimen, we could rebuild a clean image of the structure. This wouild be a used in an assay screening a bizillion flies, so SEM is not really practical. thanks, Carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 |
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In reply to this post by Boswell, Carl A - (cboswell)
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Carl,
You should also check out the EDF (Extended Depth of Field) tools in Image-Pro Plus and Image-Pro Express (both made by Media Cybernetics, www.mediacy.com). Contact Media Cybernetics to find a dealer in your area, or download a demo copy of Image-Pro Express from their web site ( http://www.mediacy.com/index.aspx?page=IPEEval). Although I no longer work for Media Cybernetics, I have worked for them in the past and would be happy to answer any questions you may have about these products. Chris Tully, M.Sc. Applications Engineer Vashaw Scientific, Inc. 7429 ACC Blvd Suite 101, Raleigh, NC 27617 Voicemail & Cell: (800) 874-9986 X339 Fax: (770) 441-7837 [hidden email] www.vashaw.com On 10/5/07, Carl Boswell <[hidden email]> wrote: Search the CONFOCAL archive at |
 
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George McNamara |
Re: software ... that selects only in focus portions of an image series to make a deep focus image
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In reply to this post by Boswell, Carl A - (cboswell)
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Carl, One of the earliest commercial software packages for doing this is Meyer Instruments In-Focus, http://www.meyerinst.com/html/oem/in-focus/default.htm (see especially the 4 PDFs at bottom), which can optionally run a Leica stereomicroscope Z-motor (ran inside Image Pro+, check with them on whether it can be automated to churn through a bizillion Z-series). Meyer also has a leica stereomicroscope turret for putting the macro lens directly under one of the stereo lenslets, to generate vertical views (and could have 2 macro lenses on the scope - a handy feature since duplicated by various stereo manufacturers). One of the faculty members at my place told me that Zeiss AxioVision has a software module for aligning slices on a conventional stereo Z-series (she also pointed out that the fly specimen used on the Meyer web site was severely desiccated). In addition to the other listserv responses, check out http://www.dipteristsforum.org.uk/deepfocus/DeepFocus.pdf and Goldsmith 2000 Image Analysis & Stereology, Deep Focus, http://www.wise-t.com/ias/article.php?id=29&year=2000&issue=11 (free access for both Goldsmith and a 2007 article - maybe we should all be publishing here). Reindeer Graphics, the makers of the Fovea Pro plugin for Photoshop also offer Focus Extender, http://www.reindeergraphics.com/index.php?option=com_content&task=view&id=29&Itemid=52 The principle of all (or at least most) of these packages is the same: run a variance filter on each plane in the stack; go through the computed variance stack to find the highest variance plane for each "sub-image"; use that sub-image as the result. Some of the better software must keep track of adjacent sub-images and blend results to make the result look nicer. Sadly, most vendors do not implement the direct outputting of the variance data (MetaMorph may still lack a variance command for example) or the plane number of the selected sub-image. George p.s. Meyer's In-Focus worked much better than MetaMorph (version 5.0), circa 2003. At 07:34 PM 10/5/2007, you wrote: >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > >Dea all, >Does anyone know of software that selects only in focus portions of >an image and discards the out-of-focus parts. We need to get clear >views of a curved surface (the fly eye) with a 10x objective using >reflected light. Only thin optical slices are in focus at this mag, >but if we could put together the portions that are in focus over the >entire depth of the specimen, we could rebuild a clean image of the >structure. This wouild be a used in an assay screening a bizillion >flies, so SEM is not really practical. >thanks, >Carl > >Carl A. Boswell, Ph.D. >Molecular and Cellular Biology >University of Arizona >520-954-7053 >FAX 520-621-3709 George McNamara, Ph.D. University of Miami, Miller School of Medicine Image Core Miami, FL 33010 [hidden email] [hidden email] 305-243-8436 office http://home.earthlink.net/~pubspectra/ http://home.earthlink.net/~geomcnamara/ http://www.sylvester.org/health_pro/shared_resources/index.asp (see Analytical Imaging Core Facility) |
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