NIS Elements software

[Martin Kann]

Hi everybody,

we are having an issue with the Nikon NIS Elements software (basic research package, version 3.00 build 550) controlling our fluorescent microscope camera. This is what happens: when taking multichannel images the red and blue channel of a .tiff image are switched if one opens this image with any other software than NIS elements. When looking into the .tiff file metadata, it appears that the TRITC image plane has been assigned blue color, and the DAPI plane red. Of course there are workarounds by using ImageJ or batch processing of files with the channel-mixer in photoshop. However, it annoys me that I have to touch each and every file one more time than necessary for my own work and frequently explain the workarounds to other people using the microscope. Has anyone ever come across this problem and knows a way to fix this in NIS elements' preferences? Maybe somebody even has a small piece of code (either Mac or PC) or a photoshop droplet that automates the task?
I would very much appreciate any help.

Thanks and regards

Martin

[Kurt Thorn]

I strongly suspect that this arises when you take 3 images.  
NIS-Elements saves them as a 3-channel tiff which is then interpreted by
ImageJ and other software packages as RGB tiff files.

We usually get around this by just saving each image as a separate tiff
file and then doing color overlays elsewhere or by just doing all
analysis in NIS-Elements.

Kurt

Martin Kann wrote:
> Hi everybody,
>
> we are having an issue with the Nikon NIS Elements software (basic research package, version 3.00 build 550) controlling our fluorescent microscope camera. This is what happens: when taking multichannel images the red and blue channel of a .tiff image are switched if one opens this image with any other software than NIS elements. When looking into the .tiff file metadata, it appears that the TRITC image plane has been assigned blue color, and the DAPI plane red. Of course there are workarounds by using ImageJ or batch processing of files with the channel-mixer in photoshop. However, it annoys me that I have to touch each and every file one more time than necessary for my own work and frequently explain the workarounds to other people using the microscope. Has anyone ever come across this problem and knows a way to fix this in NIS elements' preferences? Maybe somebody even has a small piece of code (either Mac or PC) or a photoshop droplet that automates the task?
> I would very much appreciate any help.
>
> Thanks and regards
>
> Martin
>  

[Glen MacDonald-2]

This is encountered when the acquisition software collects the images in a non-RGB manner, such as in order of shortest wavelength first and longest wavelength last.  Software that is not aware of the channel order will display the image with the RGB convention where the first image in the series is assigned to the Red LUT.  Maybe you can change the order in which channels are saved in the preferences of Elements.  You can batch convert in ImageJ by splitting the channels and re-merging in the desired order.  I've got a macro that uses the LOCI plugin to open an image into a user-selected channel order.  Also auto-saves the result.  It is not been tested with an NIS image, only on OIF, OIB and TIFF, but i can send you a copy.

Regards,
Glen  
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]




On Dec 4, 2009, at 12:57 PM, Martin Kann wrote:

> Hi everybody,
>
> we are having an issue with the Nikon NIS Elements software (basic research package, version 3.00 build 550) controlling our fluorescent microscope camera. This is what happens: when taking multichannel images the red and blue channel of a .tiff image are switched if one opens this image with any other software than NIS elements. When looking into the .tiff file metadata, it appears that the TRITC image plane has been assigned blue color, and the DAPI plane red. Of course there are workarounds by using ImageJ or batch processing of files with the channel-mixer in photoshop. However, it annoys me that I have to touch each and every file one more time than necessary for my own work and frequently explain the workarounds to other people using the microscope. Has anyone ever come across this problem and knows a way to fix this in NIS elements' preferences? Maybe somebody even has a small piece of code (either Mac or PC) or a photoshop droplet that automates the task?
> I would very much appreciate any help.
>
> Thanks and regards
>
> Martin