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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Does anyone know if a browser for the Nikon NLS Elements
.nd2 files exist? Many thanks, Xuan Xuan Chi Postdoctoral Fellow Dr. Frank Costantini lab 701 W. 168th St., HHSC1416 Columbia University Medical Center New York, NY 10032 Phone: (212)305-7911 Fax:
(212)202-2931 |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Dear Xuan,
Unfortunately there is not one available at this stage. I believe someone is about to release a plugin for ImageJ soon. So I would look out for that.
Cheers Stephen H. Cody Tip: Learn how to receive reminders about you microscope
booking: -----Original Message-----
Does anyone know if a browser for the Nikon NLS Elements .nd2 files exist?
Many thanks, Xuan
Xuan Chi Postdoctoral Fellow Dr. Frank Costantini lab 701 W. 168th St., HHSC1416 Columbia University Medical Center New York, NY 10032 Phone: (212)305-7911 Fax: (212)202-2931
This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research does not waiver any rights if you have received this communication in error. The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research. |
 
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Lambright, Geoffrey |
Re: Nikon NIS Elements Browser
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Supposedly the Bio-Formats plug-in for ImageJ will recognize ND2
files, though I have not tried it myself yet. The Bio-Formats website is: http://www.loci.wisc.edu/ome/formats.html. Geoff From: Confocal Microscopy
List [mailto:[hidden email]] On Behalf Of Stephen Cody Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Xuan, Unfortunately there is not one available at this stage. I believe
someone is about to release a plugin for ImageJ soon. So I would look out for
that. Cheers Stephen
H. Cody Tip:
Learn how to receive reminders about you microscope booking: -----Original
Message----- Does
anyone know if a browser for the Nikon NLS Elements .nd2 files exist? Many
thanks, Xuan
Xuan Chi Postdoctoral Fellow Dr. Frank Costantini lab 701 W. 168th St., HHSC1416 Columbia University Medical Center New York, NY 10032 Phone: (212)305-7911 Fax: (212)202-2931 This communication is intended only for the named recipient
and may contain information that is confidential, legally privileged or subject
to copyright; the Ludwig Institute for Cancer Research does not waiver any
rights if you have received this communication in error. |
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Kevin W Eliceiri |
Re: Nikon NIS Elements Browser
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In reply to this post by Stephen Cody
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal ImageJ with the Bio-formats plugin can open .nd2 files. See http://www.loci.wisc.edu/ome/formats.html for details. best, kevin Kevin W. Eliceiri Director Laboratory for Optical and Computational Instrumentation http://www.loci.wisc.edu Room 271 Animal Sciences 1675 Observatory Drive Madison, WI 53706 Phone: 608-263-6288 Fax: 608-262-4570 ----- Original Message ----- From: Stephen Cody <[hidden email]> Date: Tuesday, September 11, 2007 6:36 pm Subject: Nikon NIS Elements Browser To: [hidden email] > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dear Xuan, > > > > Unfortunately there is not one available at this stage. I believe > someone is about to release a plugin for ImageJ soon. So I would look > out for that. > > > > Cheers > > Stephen H. Cody > Microscopy Manager > Central Resource for Advanced Microscopy > Ludwig Institute for Cancer Research > PO Box 2008 Royal Melbourne Hospital > Parkville, Victoria, 3050 > Australia > Tel: 61 3 9341 3155 Fax: 61 3 9341 3104 > email: [hidden email] < > www.ludwig.edu.au/labs/confocal.html > < > www.ludwig.edu.au/confocal < > > Tip: Learn how to receive reminders about you microscope booking: > http://www.ludwig.edu.au/confocal/Local/Booking_Hint.htm > > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] > On > Behalf Of Xuan > Sent: Wednesday, 12 September 2007 8:25 AM > To: [hidden email] > Subject: > > > > Does anyone know if a browser for the Nikon NLS Elements .nd2 files > exist? > > > > Many thanks, > > Xuan > > > > Xuan Chi > > Postdoctoral Fellow > > Dr. Frank Costantini lab > > 701 W. 168th St., HHSC1416 > > Columbia University Medical Center > > New York, NY 10032 > > Phone: (212)305-7911 > > Fax: (212)202-2931 > > [hidden email] > > > > > > > > > > > > > > This communication is intended only for the named recipient and may > contain information that is confidential, legally privileged or > subject to copyright; the Ludwig Institute for Cancer Research does > not waiver any rights if you have received this communication in error. > The views expressed in this communication are those of the sender and > do not necessarily reflect the views of the Ludwig Institute for > Cancer Research. > |
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Jacqueline Ross |
Re: Nikon NIS Elements Browser
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In reply to this post by Stephen Cody
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Dear Xuan, Try ImageJ and the Bio-formats plugin at: http://www.loci.wisc.edu/ome/formats.html
It is listed as supporting Nikon Elements .nds files. Kind regards, Jacqui Jacqueline Ross From: Confocal
Microscopy List [mailto:[hidden email]] On Behalf Of Stephen Cody Dear Xuan, Unfortunately there is not one available
at this stage. I believe someone is about to release a plugin for ImageJ soon.
So I would look out for that. Cheers Stephen H. Cody Tip: Learn how to receive reminders about you microscope
booking: -----Original Message----- Does anyone know if a browser for the Nikon NLS Elements
.nd2 files exist? Many thanks, Xuan Xuan Chi Postdoctoral Fellow Dr. Frank Costantini lab 701 Phone: (212)305-7911 Fax: (212)202-2931 This communication is intended only for the named recipient and may
contain information that is confidential, legally privileged or subject to
copyright; the Ludwig Institute for Cancer Research does not waiver any rights
if you have received this communication in error. |
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Kevin Braeckmans |
Re: Nikon NIS Elements Browser
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In reply to this post by Kevin W Eliceiri
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I have tried this before, but it doesn't seem to work, at least not with nd2 files created on recent versions of NIS Elements (v2.2 and later). I do not know about older versions. Did anyone have better luck with this? I 'have been told' that a free Nikon nd2 browser probably will be released by the end of this year. There (hopefully!) should also be the possibility of exporting nd2 to multi-page tiff. Maybe someone can give a confirmation on this? Best regards, Kevin Kevin Braeckmans, Ph.D. Lab. General Biochemistry and Physical Pharmacy Ghent University Harelbekestraat 72 9000 Ghent Belgium Tel: +32 (0)9 264.80.78 Fax: +32 (0)9 264.81.89 > -----Oorspronkelijk bericht----- > Van: Confocal Microscopy List [mailto:[hidden email]] > Namens Kevin W Eliceiri > Verzonden: woensdag 12 september 2007 1:48 > Aan: [hidden email] > Onderwerp: Re: Nikon NIS Elements Browser > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > ImageJ with the Bio-formats plugin can open .nd2 files. See > http://www.loci.wisc.edu/ome/formats.html for details. > > best, > kevin > > Kevin W. Eliceiri > Director > Laboratory for Optical and Computational Instrumentation > http://www.loci.wisc.edu > Room 271 Animal Sciences > 1675 Observatory Drive > Madison, WI 53706 > Phone: 608-263-6288 > Fax: 608-262-4570 > > ----- Original Message ----- > From: Stephen Cody <[hidden email]> > Date: Tuesday, September 11, 2007 6:36 pm > Subject: Nikon NIS Elements Browser > To: [hidden email] > > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > > > Dear Xuan, > > > > > > > > Unfortunately there is not one available at this stage. I believe > > someone is about to release a plugin for ImageJ soon. So I would look > > out for that. > > > > > > > > Cheers > > > > Stephen H. Cody > > Microscopy Manager > > Central Resource for Advanced Microscopy > > Ludwig Institute for Cancer Research > > PO Box 2008 Royal Melbourne Hospital > > Parkville, Victoria, 3050 > > Australia > > Tel: 61 3 9341 3155 Fax: 61 3 9341 3104 > > email: [hidden email] < > > www.ludwig.edu.au/labs/confocal.html > > < > > www.ludwig.edu.au/confocal < > > > > Tip: Learn how to receive reminders about you microscope booking: > > http://www.ludwig.edu.au/confocal/Local/Booking_Hint.htm > > > > -----Original Message----- > > From: Confocal Microscopy List [mailto:[hidden email]] > > On > > Behalf Of Xuan > > Sent: Wednesday, 12 September 2007 8:25 AM > > To: [hidden email] > > Subject: > > > > > > > > Does anyone know if a browser for the Nikon NLS Elements .nd2 files > > exist? > > > > > > > > Many thanks, > > > > Xuan > > > > > > > > Xuan Chi > > > > Postdoctoral Fellow > > > > Dr. Frank Costantini lab > > > > 701 W. 168th St., HHSC1416 > > > > Columbia University Medical Center > > > > New York, NY 10032 > > > > Phone: (212)305-7911 > > > > Fax: (212)202-2931 > > > > [hidden email] > > > > > > > > > > > > > > > > > > > > > > > > > > > > This communication is intended only for the named recipient and may > > contain information that is confidential, legally privileged or > > subject to copyright; the Ludwig Institute for Cancer Research does > > not waiver any rights if you have received this communication in > error. > > The views expressed in this communication are those of the sender and > > do not necessarily reflect the views of the Ludwig Institute for > > Cancer Research. > > |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Kevin, I've had similar experiences with the LOCI opener and ND2 image format. Stephen H. Cody Microscopy Manager Central Resource for Advanced Microscopy Ludwig Institute for Cancer Research PO Box 2008 Royal Melbourne Hospital Parkville, Victoria, 3050 Australia Tel: 61 3 9341 3155 Fax: 61 3 9341 3104 email: [hidden email] www.ludwig.edu.au/labs/confocal.html www.ludwig.edu.au/confocal This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research does not waiver any rights if you have received this communication in error. The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research. |
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Kevin W Eliceiri |
Re: Nikon NIS Elements Browser
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Stephen and Kevin, As the .nd2 format is not a open file format and we don't yet have file specifications from Nikon, its accurate support in Bio-formats is completely dependent on community input and feedback. There was a new release of Bio-formats yesterday that should fix the .nd2 issues. I have the latest version of Elements and it does appear to work with these files. Please try this and let the Bio-formats developers know if any problems (contact info on the webpage). I should add Bio-formats is more than a file viewer plug-in for ImageJ, its a community project to develop a library for viewing and mapping proprietary file formats (have done 50 so far) to the OME-TIFF standard (www.ome-xml.org). The Bio-formats plugin is used by several applications including ImageJ, VisBio, and the OME databases. To make this effort work we really do need help from the microscopy community in the form of letting us know when formats change, other bugs in the import/mapping process and to encourage com mercial vendor support. Please feel free to contact us directly if you have desired changes/additions for Bio-formats or if you are interested in joining the development effort. best, kevin Kevin W. Eliceiri Director Laboratory for Optical and Computational Instrumentation http://www.loci.wisc.edu Room 271 Animal Sciences 1675 Observatory Drive Madison, WI 53706 Phone: 608-263-6288 Fax: 608-262-4570 ----- Original Message ----- From: Stephen Cody <[hidden email]> Date: Wednesday, September 12, 2007 2:42 am Subject: Re: Nikon NIS Elements Browser To: [hidden email] > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dear Kevin, > > I've had similar experiences with the LOCI opener and ND2 image format. > > Stephen H. Cody > Microscopy Manager > Central Resource for Advanced Microscopy > Ludwig Institute for Cancer Research > PO Box 2008 Royal Melbourne Hospital > Parkville, Victoria, 3050 > Australia > Tel: 61 3 9341 3155 Fax: 61 3 9341 3104 > email: [hidden email] > www.ludwig.edu.au/labs/confocal.html > www.ludwig.edu.au/confocal > > > > This communication is intended only for the named recipient and may > contain information that is confidential, legally privileged or > subject to copyright; the Ludwig Institute for Cancer Research does > not waiver any rights if you have received this communication in error. > The views expressed in this communication are those of the sender and > do not necessarily reflect the views of the Ludwig Institute for > Cancer Research. > |
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In reply to this post by Stephen Cody
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Kevin et al., I believe that instrument manufacturers should become much better at opening up file formats, and facilitating format conversions. This is such an unnecessary hassle for the user community. In this regard. your open-source Bio-formats effort is particularly admirable. It would make sense for instrtument developers to participate in OME, at least to ensure that their file formats are handled correctly! Badri Roysam Professor, Department of Electrical, Computer and Systems Engineering Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC) Rensselaer Polytechnic Institute 110 8th Street, Troy, New York 12180-3590. Office(JEC 7010): 518-276-8067, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715 Email: [hidden email], Web: http://www.ecse.rpi.edu/~roysam ----- Original Message ----- From: Kevin W Eliceiri [mailto:[hidden email]] To: [hidden email] Subject: Re: Nikon NIS Elements Browser > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dear Stephen and Kevin, > > As the .nd2 format is not a open file format and we don't yet have file > specifications from Nikon, its accurate support in Bio-formats is completely > dependent on community input and feedback. There was a new release of > Bio-formats yesterday that should fix the .nd2 issues. I have the latest > version of Elements and it does appear to work with these files. Please try > this and let the Bio-formats developers know if any problems (contact info > on the webpage). I should add Bio-formats is more than a file viewer > plug-in for ImageJ, its a community project to develop a library for viewing > and mapping proprietary file formats (have done 50 so far) to the OME-TIFF > standard (www.ome-xml.org). The Bio-formats plugin is used by several > applications including ImageJ, VisBio, and the OME databases. To make this > effort work we really do need help from the microscopy community in the form > of letting us know when formats change, other bugs in the import/mapping > process and to encourage com > mercial vendor support. Please feel free to contact us directly if you have > desired changes/additions for Bio-formats or if you are interested in > joining the development effort. > > best, > kevin > > > Kevin W. Eliceiri > Director > Laboratory for Optical and Computational Instrumentation > http://www.loci.wisc.edu > Room 271 Animal Sciences > 1675 Observatory Drive > Madison, WI 53706 > Phone: 608-263-6288 > Fax: 608-262-4570 > > ----- Original Message ----- > From: Stephen Cody <[hidden email]> > Date: Wednesday, September 12, 2007 2:42 am > Subject: Re: Nikon NIS Elements Browser > To: [hidden email] > > > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > > > Dear Kevin, > > > > I've had similar experiences with the LOCI opener and ND2 image format. > > > > Stephen H. Cody > > Microscopy Manager > > Central Resource for Advanced Microscopy > > Ludwig Institute for Cancer Research > > PO Box 2008 Royal Melbourne Hospital > > Parkville, Victoria, 3050 > > Australia > > Tel: 61 3 9341 3155 Fax: 61 3 9341 3104 > > email: [hidden email] > > www.ludwig.edu.au/labs/confocal.html > > www.ludwig.edu.au/confocal > > > > > > > > This communication is intended only for the named recipient and may > > contain information that is confidential, legally privileged or > > subject to copyright; the Ludwig Institute for Cancer Research does > > not waiver any rights if you have received this communication in error. > > The views expressed in this communication are those of the sender and > > do not necessarily reflect the views of the Ludwig Institute for > > Cancer Research. > > > |
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Kevin Braeckmans |
Re: Nikon NIS Elements Browser
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In reply to this post by Kevin W Eliceiri
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Kevin, I have tried the new ImageJ plug-in and opening the nd2 files seems to be working fine now. Thanks to the developers and the Bio-formats community - that is a really big help to us! Thanks, Kevin Kevin Braeckmans, Ph.D. Lab. General Biochemistry and Physical Pharmacy Ghent University Harelbekestraat 72 9000 Ghent Belgium Tel: +32 (0)9 264.80.78 Fax: +32 (0)9 264.81.89 > -----Oorspronkelijk bericht----- > Van: Confocal Microscopy List [mailto:[hidden email]] > Namens Kevin W Eliceiri > Verzonden: woensdag 12 september 2007 13:47 > Aan: [hidden email] > Onderwerp: Re: Nikon NIS Elements Browser > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Dear Stephen and Kevin, > > As the .nd2 format is not a open file format and we don't yet have file > specifications from Nikon, its accurate support in Bio-formats is > completely dependent on community input and feedback. There was a new > release of Bio-formats yesterday that should fix the .nd2 issues. I > have the latest version of Elements and it does appear to work with > these files. Please try this and let the Bio-formats developers know if > any problems (contact info on the webpage). I should add Bio-formats > is more than a file viewer plug-in for ImageJ, its a community project > to develop a library for viewing and mapping proprietary file formats > (have done 50 so far) to the OME-TIFF standard (www.ome-xml.org). The > Bio-formats plugin is used by several applications including ImageJ, > VisBio, and the OME databases. To make this effort work we really do > need help from the microscopy community in the form of letting us know > when formats change, other bugs in the import/mapping process and to > encourage com > mercial vendor support. Please feel free to contact us directly if you > have desired changes/additions for Bio-formats or if you are interested > in joining the development effort. > > best, > kevin > > > Kevin W. Eliceiri > Director > Laboratory for Optical and Computational Instrumentation > http://www.loci.wisc.edu > Room 271 Animal Sciences > 1675 Observatory Drive > Madison, WI 53706 > Phone: 608-263-6288 > Fax: 608-262-4570 > > ----- Original Message ----- > From: Stephen Cody <[hidden email]> > Date: Wednesday, September 12, 2007 2:42 am > Subject: Re: Nikon NIS Elements Browser > To: [hidden email] > > > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > > > Dear Kevin, > > > > I've had similar experiences with the LOCI opener and ND2 image > format. > > > > Stephen H. Cody > > Microscopy Manager > > Central Resource for Advanced Microscopy > > Ludwig Institute for Cancer Research > > PO Box 2008 Royal Melbourne Hospital > > Parkville, Victoria, 3050 > > Australia > > Tel: 61 3 9341 3155 Fax: 61 3 9341 3104 > > email: [hidden email] > > www.ludwig.edu.au/labs/confocal.html > > www.ludwig.edu.au/confocal > > > > > > > > This communication is intended only for the named recipient and may > > contain information that is confidential, legally privileged or > > subject to copyright; the Ludwig Institute for Cancer Research does > > not waiver any rights if you have received this communication in > error. > > The views expressed in this communication are those of the sender and > > do not necessarily reflect the views of the Ludwig Institute for > > Cancer Research. > > |
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