Problem opening Nikon Elements files
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Problem opening Nikon Elements files
 
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We are having problems opening NIS 3.0 files and hope that somebody has a solution.
We are collecting four 16 bit images, three fluorescent probes and a brightfield image of fixed and stained cells. When we try to open them in ImageJ, they make a weird multicolor image. When we open in Photoshop, the first image in the series opens properly as a 16 bit grayscale, but the other images in the sequence are not accessible. ( see http://www.flickr.com/photos/mcammer/5220769893/sizes/l/ for screen snap) There are two ways we have tried to save the files and each has a different odd result. One way is to save each individually as a TIFF. In this case, the file size is 2,236,838 bytes. (left image in screensnap) The second way is to have each sequence of four saved as the images are collected. In this case, we specify the format to be Nikon's, but the file is saved with a TIF extension. Renaming the tiff extension does not solve the problem. The file size is 2,322,552 bytes. (right image in screensnap) The LOCI importer, which works fine on the Nikon Z and time series sequences, chokes on these files or opens them with the same weird colors as ImageJ directly. Any help appreciated! Thank you. ________________________________________________________ Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine Lab: (212) 263-3208 Cell: (914) 309-3270 </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE> |
Re: Problem opening Nikon Elements files
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More information on the problem:
If there are only three channels in the image it opens as a 16 bit RGB stack. If there is one image, it opens as it should as a 16 bit single image. Any other numbers of channels gives the error "Unsupported SamplesPerPixel: #" Is there a way to open a file of any number into a simple 16 bit stack? Thanks! -Michael From: Cammer, Michael Sent: Tuesday, November 30, 2010 11:55 AM To: [hidden email] Cc: 'Keith Gembala'; Liapis, Anastasia Subject: Problem opening Nikon ECammer, Michaellements files We are having problems opening NIS 3.0 files and hope that somebody has a solution. We are collecting four 16 bit images, three fluorescent probes and a brightfield image of fixed and stained cells. When we try to open them in ImageJ, they make a weird multicolor image. When we open in Photoshop, the first image in the series opens properly as a 16 bit grayscale, but the other images in the sequence are not accessible. ( see http://www.flickr.com/photos/mcammer/5220769893/sizes/l/ for screen snap) There are two ways we have tried to save the files and each has a different odd result. One way is to save each individually as a TIFF. In this case, the file size is 2,236,838 bytes. (left image in screensnap) The second way is to have each sequence of four saved as the images are collected. In this case, we specify the format to be Nikon's, but the file is saved with a TIF extension. Renaming the tiff extension does not solve the problem. The file size is 2,322,552 bytes. (right image in screensnap) The LOCI importer, which works fine on the Nikon Z and time series sequences, chokes on these files or opens them with the same weird colors as ImageJ directly. Any help appreciated! Thank you. ________________________________________________________ Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine Lab: (212) 263-3208 Cell: (914) 309-3270 </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE> |
Re: Problem opening Nikon Elements files
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I faced this issue a while ago, I no longer use NIS on a daily basis (changed work place), however I remember we got a macro for NIS (one of the Nikon reps installed it). It basically generated a sequence of monochrome 16-bit tiff files which could be read with image J with no problems and joined into a stack or multichannel image in the usual way. Hope this helps somehow.
Leoncio -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Cammer, Michael Sent: Tuesday, November 30, 2010 11:22 AM To: [hidden email] Subject: Re: Problem opening Nikon Elements files More information on the problem: If there are only three channels in the image it opens as a 16 bit RGB stack. If there is one image, it opens as it should as a 16 bit single image. Any other numbers of channels gives the error "Unsupported SamplesPerPixel: #" Is there a way to open a file of any number into a simple 16 bit stack? Thanks! -Michael From: Cammer, Michael Sent: Tuesday, November 30, 2010 11:55 AM To: [hidden email] Cc: 'Keith Gembala'; Liapis, Anastasia Subject: Problem opening Nikon ECammer, Michaellements files We are having problems opening NIS 3.0 files and hope that somebody has a solution. We are collecting four 16 bit images, three fluorescent probes and a brightfield image of fixed and stained cells. When we try to open them in ImageJ, they make a weird multicolor image. When we open in Photoshop, the first image in the series opens properly as a 16 bit grayscale, but the other images in the sequence are not accessible. ( see http://www.flickr.com/photos/mcammer/5220769893/sizes/l/ for screen snap) There are two ways we have tried to save the files and each has a different odd result. One way is to save each individually as a TIFF. In this case, the file size is 2,236,838 bytes. (left image in screensnap) The second way is to have each sequence of four saved as the images are collected. In this case, we specify the format to be Nikon's, but the file is saved with a TIF extension. Renaming the tiff extension does not solve the problem. The file size is 2,322,552 bytes. (right image in screensnap) The LOCI importer, which works fine on the Nikon Z and time series sequences, chokes on these files or opens them with the same weird colors as ImageJ directly. Any help appreciated! Thank you. ________________________________________________________ Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine Lab: (212) 263-3208 Cell: (914) 309-3270 </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE> |
Re: Problem opening Nikon Elements files
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In reply to this post by Cammer, Michael
Have you tried sending them to the LOCI support people? I have found them to be very responsive to such problems. They will give you a link to upload the problem file and a fix in the next daily build. Dave
On Nov 30, 2010, at 11:55 AM, Cammer, Michael wrote: > We are having problems opening NIS 3.0 files and hope that somebody has a solution. > > We are collecting four 16 bit images, three fluorescent probes and a brightfield image of fixed and stained cells. When we try to open them in ImageJ, they make a weird multicolor image. When we open in Photoshop, the first image in the series opens properly as a 16 bit grayscale, but the other images in the sequence are not accessible. ( see http://www.flickr.com/photos/mcammer/5220769893/sizes/l/ for screen snap) > > There are two ways we have tried to save the files and each has a different odd result. > > One way is to save each individually as a TIFF. In this case, the file size is 2,236,838 bytes. (left image in screensnap) > > The second way is to have each sequence of four saved as the images are collected. In this case, we specify the format to be Nikon's, but the file is saved with a TIF extension. Renaming the tiff extension does not solve the problem. The file size is 2,322,552 bytes. (right image in screensnap) > > The LOCI importer, which works fine on the Nikon Z and time series sequences, chokes on these files or opens them with the same weird colors as ImageJ directly. > > Any help appreciated! > > Thank you. > > > > ________________________________________________________ > Michael Cammer, Assistant Research Scientist > Skirball Institute of Biomolecular Medicine > Lab: (212) 263-3208 Cell: (914) 309-3270 > > </PRE> > <html> > <body> > ------------------------------------------------------------<br /> > This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> > ================================= > </body> > </html> > <PRE> Dr. David Knecht Department of Molecular and Cell Biology Co-head Flow Cytometry and Confocal Microscopy Facility U-3125 91 N. Eagleville Rd. University of Connecticut Storrs, CT 06269 860-486-2200 860-486-4331 (fax) |
Re: Problem opening Nikon Elements files
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In reply to this post by Cammer, Michael
Hi Michael,
> The LOCI importer, which works fine on the Nikon Z and time series sequences, chokes on these files or opens them with the same weird colors as ImageJ directly. I would first recommend making sure that you have the latest stable release of Bio-Formats (4.2.1). You can see which version is installed in ImageJ by selecting "Help > About Plugins > LOCI Plugins". If you see the problem with 4.2.1, then it is certainly something that we would fix in Bio-Formats; unfortunately, it is a bit difficult to fix without seeing one of the problematic files. I have sent you a private email with instructions for sending files to us (the Bio-Formats developers), in case you are interested in providing an example file. Regards, -Melissa On Tue, Nov 30, 2010 at 12:22:25PM -0500, Cammer, Michael wrote: > More information on the problem: > > If there are only three channels in the image it opens as a 16 bit RGB stack. If there is one image, it opens as it should as a 16 bit single image. Any other numbers of channels gives the error "Unsupported SamplesPerPixel: #" > > Is there a way to open a file of any number into a simple 16 bit stack? > > Thanks! > > -Michael > > From: Cammer, Michael > Sent: Tuesday, November 30, 2010 11:55 AM > To: [hidden email] > Cc: 'Keith Gembala'; Liapis, Anastasia > Subject: Problem opening Nikon ECammer, Michaellements files > > We are having problems opening NIS 3.0 files and hope that somebody has a solution. > > We are collecting four 16 bit images, three fluorescent probes and a brightfield image of fixed and stained cells. When we try to open them in ImageJ, they make a weird multicolor image. When we open in Photoshop, the first image in the series opens properly as a 16 bit grayscale, but the other images in the sequence are not accessible. ( see http://www.flickr.com/photos/mcammer/5220769893/sizes/l/ for screen snap) > > There are two ways we have tried to save the files and each has a different odd result. > > One way is to save each individually as a TIFF. In this case, the file size is 2,236,838 bytes. (left image in screensnap) > > The second way is to have each sequence of four saved as the images are collected. In this case, we specify the format to be Nikon's, but the file is saved with a TIF extension. Renaming the tiff extension does not solve the problem. The file size is 2,322,552 bytes. (right image in screensnap) > > The LOCI importer, which works fine on the Nikon Z and time series sequences, chokes on these files or opens them with the same weird colors as ImageJ directly. > > Any help appreciated! > > Thank you. > > > > ________________________________________________________ > Michael Cammer, Assistant Research Scientist > Skirball Institute of Biomolecular Medicine > Lab: (212) 263-3208 Cell: (914) 309-3270 > > </PRE> > <html> > <body> > ------------------------------------------------------------<br /> > This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> > ================================= > </body> > </html> > <PRE> |
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