Graphing filter/fluorphore spectra...
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Jennifer Waters |
Graphing filter/fluorphore spectra...
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Search the CONFOCAL archive at
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What is your favorite online program for graphing filter & fluorophore spectra? I currently use: http://fluorescence.nexus-solutions.net/frames6.htm Best, Jennifer -- Jennifer Waters, Ph.D. Director, Nikon Imaging Center at Harvard Medical School |
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Valeria Berno |
Re: Graphing filter/fluorphore spectra...
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi, I think the best I ever found is the Molecular probes one http://probes.invitrogen.com/resources/spectraviewer/ no commercial interest valeria Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > What is your favorite online program for graphing filter & fluorophore > spectra? I currently use: > > http://fluorescence.nexus-solutions.net/frames6.htm > > Best, Jennifer > > -- > Jennifer Waters, Ph.D. > Director, Nikon Imaging Center at Harvard Medical School > |
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Michael Weber-4 |
Re: Graphing filter/fluorphore spectra...
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In reply to this post by Jennifer Waters
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Jennifer, I like the search function of the Bio-Rad database, but the layout is not very intuitive. That's why I usually prefer the one from Invitrogen, even if the simple fluorophore list is horoble: http://probes.invitrogen.com/resources/spectraviewer/ But these one's are also nice: http://www.mcb.arizona.edu/ipc/fret/index.html http://www.bdbiosciences.com/spectra/ cheers, Michael Jennifer Waters wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > What is your favorite online program for graphing filter & fluorophore > spectra? I currently use: > > http://fluorescence.nexus-solutions.net/frames6.htm > <http://fluorescence.nexus-solutions.net/frames6.htm> > > Best, Jennifer > > -- > Jennifer Waters, Ph.D. > Director, Nikon Imaging Center at Harvard Medical School |
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Dries Vercauteren |
Re: Graphing filter/fluorphore spectra...
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In reply to this post by Jennifer Waters
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Dear all, the ones I know and use are; <a href="http://www.olympusconfocal.com/java/dualprobes/index.html" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.olympusconfocal.com/java/dualprobes/index.html <a href="http://www.mcb.arizona.edu/IPC/spectra_page.htm" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://www.mcb.arizona.edu/IPC/spectra_page.htm <a href="http://www.mcb.arizona.edu/ipc/fret/index.html" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.mcb.arizona.edu/ipc/fret/index.html and of course the Mol Probes one; <a href="http://probes.invitrogen.com/resources/spectraviewer/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://probes.invitrogen.com/resources/spectraviewer/ Cheers, Dries. On 15/01/2008, Jennifer Waters <[hidden email]> wrote: Search the CONFOCAL archive at <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal -- Dries Vercauteren, PhD student Master of Bioscience Engineering: Cell and Gene Biotechnology Ghent Research Group on Nanomedicines www.ugent.be/fw/en/research/biofys Faculty of pharmaceutical sciences, Ghent University Harelbekestraat 72, 9000 Ghent Belgium Phone: +329/264 80 49 Mobile: +32485/30 69 80 E-mail: [hidden email] [hidden email] |
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In reply to this post by Jennifer Waters
Search the CONFOCAL archive at
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I use; in this order; http://probes.invitrogen.com/resources/spectraviewer/ http://www.bdbiosciences.com/spectra/ http://www.mcb.arizona.edu/IPC/spectra_page.htm I stand corrected regarding the
introduction of Coherent’s new GVD compensation equipment. I guess they DO think that the GVD problem
is worth addressing (or at least that they should address Spectra Physic’s
Deep See option). Coherent’s new instrument is the Chameleon PreComp,
Automated Dispersion for Chameleon Ti:Sapphire Lasers. They also have a new OPO device. No commercial interest. http://www.coherent.com/Lasers/index.cfm?fuseaction=show.page&ID=1557&loc=0 Brian D Armstrong PhD Light Microscopy Core Manager Beckman Research Institute City of 626-359-8111 x62872 From: Confocal
Microscopy List [mailto:[hidden email]] On Behalf Of Jennifer Waters Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
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George McNamara |
Re: Graphing filter/fluorphore spectra...
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In reply to this post by Jennifer Waters
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UA's Fluorescent Dye Spectra web site
http://www.mcb.arizona.edu/ipc/fret/index.html summarized
in Carl's and my article in Cytometry 2006
(
Link).
I admit to occasionally using Invitrogen's spectra viewer, and still find
of use their web list version
http://probes.invitrogen.com/servlets/spectra/ Our 2006 paper points
out, data are facts, and facts are not copyrightable (in the USA, at
least), so their statement "Molecular Probes will grant
copyright authorization for reproduction of these spectra in research
publications and for other non-commercial uses." is moot.
When I need more than a graph in a browser I launch Excel and do more graphing and number crunching as needed from the source data, which is available at PubSpectra http://home.earthlink.net/~pubspectra/ Index file for the whole dataset: McNamara_Boswell_000_2006_Index _Dyes_FPs_Filters_Lamps_Other_Spectra.xls 1314 Fluorescent dyes and fluorescent proteins spectra: McNamara_Boswell_Spectra_Dyes_FPs.zip 966 Filters spectra: McNamara_Boswell_Spectra_Filters .zip 99 Light sources and other spectra: McNamara_Boswell_Spectra_Lamps_other .zip Janos Szollosi and Horvath Gabor sent me an Excel FRET calculator, that I have modified slightly: http://home.earthlink.net/~fluorescentdyes/McNamara 20050709 FRET Janos Szollosi Horvath Gabor FRET calculator .xls Some day I will transfer all the data of each class into a single Excel 2007 "big grid" sheet and re-post it. Memo to Chroma, Omega, Semrock and other filter manufacturers: we are pretty close to an even 1000 filter spectra. If you've come up with any new filters in the past 2 years, please email them (or their web links) to me. Text files (zipped up) or Excel file, please. I'll deal with getting them into standard format. Anyone who has acquired accurate spectra of dyes - especially new dyes - I would love to have your data for addition to PubSpectra and UA (accurate means spectrophotometer, spectrofluorometer, or PARISS - you can post META and similar low resolution data on your own web site). Now that I am co-manager of a multiphoton fluorescence microscope, I would especially love to have multiphoton spectra. I have various graphs but would like data. If anyone enjoyed (or at least read) our 2006 Cytometry article, you may also find of interest: A Thousand Proteins of Light: 15 Years of Advances in Fluorescent Proteins G. McNamara and C.A. Boswell posted at Formatex microscopy3 website a couple of weeks ago. See http://www.formatex.org/microscopy3/papers.htm for all the articles (free online access). I especially liked Super-Quiet Microfluorometry: Examples of Tumor Cell Metabolic Dynamics A.J. Clark and H.R. Petty Some of the fluorescence articles are near the bottom of the contents page: Semiconductor nanocrystals and fluorescence microscopy in biological labeling P.M.A. Farias, B.S. Santos, A.Fontes and C.L. Cesar Fluorescence Correlation Spectroscopy of Living Cells G. Vereb, L. Ujlaky-Nagy, E. Friedländer G. Vámosi and J. Szöll si Fluorescence Correlation Spectroscopy: an Experimentalists View of the Basics G. Jung Linear fluorescence unmixing in cell biological research B. Kraus, M. Ziegler and H. Wolff High resolution Near-field Fluorescence Microscopy: from principles to applications in cell biology A. Cambi, C.G. Figdor and M.F. Garcia-Parajo Two-Photon Fluorescence Microscopy: Basic Principles, Advantages and Risks S.J. Mulligan and B.A. MacVicar Colours Count: how the Challenge of Fluorescence was solved in Confocal Microscopy R. Borlinghaus (Leica's version of history) Software-based three dimensional reconstructions and enhancements of focal depth in microphotographic images J. Piper Digital Deconvolution Microscopy: Development, Evaluation and Utilization in 3D quantitative studies of E-cadherin expression in skin of Bufo arenarun tadpoles J.F. Adur, J.E. Diaz-Zamboni, N.B. Vicente, M.F. Izaguirre and V.H. Casco Concurrent 3-D Visualization of Multiple Microscopic Structures S.J. Rehorek and T.D. Smith At 10:55 AM 1/15/2008, you wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal 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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Michael Weber-4 |
post-correction of line-shift induced by bi-directional point scan?
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear all, this question is about the use of bi-directional scan mode with a Zeiss LSM 510. In one of our setups we use this mode to get the necessary fps with a 40x/1.2 W objective, 512x200, "zoom 4" and "scan speed 12". Unfortunately we cannot manage to fully correct the shift in X, which means that a shift of 1 pixel remains whatever you do. Scanner calibration (with 10x/0.45) also doesn't help. My question is: Does a tool exist with which I can correct for this shift afterwards? To my understanding this is quite simple - just shift every second line by x pixels to left or right. Leica has this feature implemented in their software, but this doesn't help much in case of Zeiss. Maybe somebody has a macro directly for the LSM software or a plugin for ImageJ? I would appreciate any input. Thanks! Michael |
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Rietdorf, Jens |
Re: post-correction of line-shift induced by bi-directional point scan?
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Michael, This function is available from the 'Process' menu of the LSM-software. regards, jens --- Dr. Jens Rietdorf Head Microscopy Novartis Research Foundation Friedrich-Miescher-Institute, wro1066.2.16 Maulbeerstr.66, CH-4058 Basel, Switzerland phone +41(61)69-75172 mobil +41 798284737 Email:rietdorf(at)fmi.ch -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Weber Sent: Mittwoch, 16. Januar 2008 16:41 To: [hidden email] Subject: post-correction of line-shift induced by bi-directional point scan? Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear all, this question is about the use of bi-directional scan mode with a Zeiss LSM 510. In one of our setups we use this mode to get the necessary fps with a 40x/1.2 W objective, 512x200, "zoom 4" and "scan speed 12". Unfortunately we cannot manage to fully correct the shift in X, which means that a shift of 1 pixel remains whatever you do. Scanner calibration (with 10x/0.45) also doesn't help. My question is: Does a tool exist with which I can correct for this shift afterwards? To my understanding this is quite simple - just shift every second line by x pixels to left or right. Leica has this feature implemented in their software, but this doesn't help much in case of Zeiss. Maybe somebody has a macro directly for the LSM software or a plugin for ImageJ? I would appreciate any input. Thanks! Michael |
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Michael Weber-4 |
Re: post-correction of line-shift induced by bi-directional point scan?
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Jens, sorry, I don't get it. In the LSM software (v4.2) one has a "Shift" function for color shift i.e. induced by lasers coupled over two fibers or misaligned pinholes. But I cannot shift every second line in a single channel - or am I overlooking something? Are you talking about the ZEN software? cheers, Michael > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dear Michael, > > This function is available from the 'Process' menu of the LSM-software. > > regards, jens > > --- > Dr. Jens Rietdorf > Head Microscopy > Novartis Research Foundation > Friedrich-Miescher-Institute, wro1066.2.16 Maulbeerstr.66, CH-4058 > Basel, Switzerland > phone +41(61)69-75172 mobil +41 798284737 > Email:rietdorf(at)fmi.ch > > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] On > Behalf Of Michael Weber > Sent: Mittwoch, 16. Januar 2008 16:41 > To: [hidden email] > Subject: post-correction of line-shift induced by bi-directional point > scan? > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dear all, > > this question is about the use of bi-directional scan mode with a Zeiss > LSM 510. In one of our setups we use this mode to get the necessary fps > with a 40x/1.2 W objective, 512x200, "zoom 4" and "scan speed 12". > Unfortunately we cannot manage to fully correct the shift in X, which > means that a shift of 1 pixel remains whatever you do. Scanner > calibration (with 10x/0.45) also doesn't help. > > My question is: Does a tool exist with which I can correct for this > shift afterwards? To my understanding this is quite simple - just shift > every second line by x pixels to left or right. Leica has this feature > implemented in their software, but this doesn't help much in case of > Zeiss. > > Maybe somebody has a macro directly for the LSM software or a plugin for > ImageJ? I would appreciate any input. > > Thanks! > Michael |
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Xuejun Sun |
Re: post-correction of line-shift induced by bi-directional point scan?
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In reply to this post by Michael Weber-4
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi, I think what you need are some tools to deal with old video camera images. Look into Deinterlace and Interlace functions in ImageJ, you should be able to separate out the odd and even lines, align them and remerge them or the module does all these together. Here is what I found with google: http://rsbweb.nih.gov/ij/plugins/de-interlace.html Alternatively, Metamorph has such tools if you do use it. I am not aware of any tools in Zeiss LSM software for such correction. What we found with our 510 (which is almost 10yrs old), was that, at high speed scanning, the scanner had significant deviations in 2 directions. So the odd/even images are distorted. The final images are not result of a uniform shifting which could be easily corrected. Good luck, Xue-jun Xue-jun Sun, Ph.D. Dept. Exp. Oncology Cross Cancer Institute 11560 University Ave, Edmonton Alberta T6G 1Z2 Canada Phone: (780) 432-8898 Fax: (780) 432-8425 -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Weber Sent: Wednesday, January 16, 2008 8:41 AM To: [hidden email] Subject: post-correction of line-shift induced by bi-directional point scan? Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear all, this question is about the use of bi-directional scan mode with a Zeiss LSM 510. In one of our setups we use this mode to get the necessary fps with a 40x/1.2 W objective, 512x200, "zoom 4" and "scan speed 12". Unfortunately we cannot manage to fully correct the shift in X, which means that a shift of 1 pixel remains whatever you do. Scanner calibration (with 10x/0.45) also doesn't help. My question is: Does a tool exist with which I can correct for this shift afterwards? To my understanding this is quite simple - just shift every second line by x pixels to left or right. Leica has this feature implemented in their software, but this doesn't help much in case of Zeiss. Maybe somebody has a macro directly for the LSM software or a plugin for ImageJ? I would appreciate any input. Thanks! Michael This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. |
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In reply to this post by Michael Weber-4
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Dear Michael,
I do these kind of things in IDL as parts of an image analysis program package that I wrote gradually over the years. May be able to provide a specialised .SAV file that can be run w/o having an IDL license (but do need IDL Virtual Machine, which is free) if you'd like and if you specifiy what you need the program to do.
Best,
Zoltan
On Jan 16, 2008 3:41 PM, Michael Weber <[hidden email]> wrote: Search the CONFOCAL archive at -- -- Zoltan Cseresnyes Facility manager, Imaging Suite Dept. of Zoology University of Cambridge Downing Street, Cambridge CB2 3EJ UK Tel.: (++44) (0)1223 769282 Fax.: (++44) (0)1223 336676 |
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In reply to this post by Michael Weber-4
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Michael, You may try this: http://rsb.info.nih.gov/ij/plugins/x-shifter.html Wish it helps. -- Best regards, Peng Xi Associate Professor Institute for Laser Medicine and Biophotonics Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240, China Tel: (86) 21-3420-4076 http://biophotonics.sjtu.edu.cn/ Michael Weber wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dear all, > > this question is about the use of bi-directional scan mode with a > Zeiss LSM 510. In one of our setups we use this mode to get the > necessary fps with a 40x/1.2 W objective, 512x200, "zoom 4" and "scan > speed 12". Unfortunately we cannot manage to fully correct the shift > in X, which means that a shift of 1 pixel remains whatever you do. > Scanner calibration (with 10x/0.45) also doesn't help. > > My question is: Does a tool exist with which I can correct for this > shift afterwards? To my understanding this is quite simple - just > shift every second line by x pixels to left or right. Leica has this > feature implemented in their software, but this doesn't help much in > case of Zeiss. > > Maybe somebody has a macro directly for the LSM software or a plugin > for ImageJ? I would appreciate any input. > > Thanks! > Michael |
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Michael Weber-4 |
Re: post-correction of line-shift induced by bi-directional point scan?
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks a lot Peng Xi, I followed another link on this page and found this one: http://rsb.info.nih.gov/ij/plugins/correct-shift.html And it works perfect! cheers, Michael Peng Xi wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi Michael, > You may try this: http://rsb.info.nih.gov/ij/plugins/x-shifter.html > Wish it helps. |
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