ImageJ Micromanager Tiff images

[Hani Mahmoud]

Hello,

I am taking 16-bit TIFF images using a Micromanager as an ImageJ plugin. I've been having a simple problem opening these TIFF images. They open fine when opened in ImageJ, but they do not open or they appear black when opened in any other program that is capable of taking TIFF images. Before using Micromanager/ImageJ, my TIFF images could be opened in any program. I need to be able to open them in programs other than ImageJ so that I can analyze the images in MATLAB. If I open each image individually with ImageJ and save the files as another filetype, like JPEG, then I can open them in any program. However, I am taking many images, so this is too tedious for my situation.

Any suggestions would be greatly appreciated.

Thank you,

Hani

[ctrueden]

Hi Hani,


I am taking 16-bit TIFF images using a Micromanager as an ImageJ plugin.
> I've been having a simple problem opening these TIFF images. They open fine
> when opened in ImageJ, but they do not open or they appear black when
> opened in any other program that is capable of taking TIFF images.
>

Chances are that your actual data values are correct—it's just the
visualization that appears all black. Since you have 16-bit images, it is
likely the data is being scaled from 0-65535, when your actual intensity
range is much lower (e.g., for a 12-bit camera, you won't have intensity
values above 4095).

You will want to autoscale your display min/max based on the data before
visualizing it. In the case of MATLAB with the imagesc function, you can
set the bounds explicitly using the clims parameter. For details, see:
http://www.mathworks.com/help/techdoc/ref/imagesc.html

Regards,
Curtis

P.S. You can use Bio-Formats to read Micro-Manager data into MATLAB; see:
   http://loci.wisc.edu/bio-formats/matlab


On Tue, Mar 27, 2012 at 8:49 PM, Hani Mahmoud <[hidden email]> wrote:

> Hello,
>
> I am taking 16-bit TIFF images using a Micromanager as an ImageJ plugin.
> I've been having a simple problem opening these TIFF images. They open fine
> when opened in ImageJ, but they do not open or they appear black when
> opened in any other program that is capable of taking TIFF images. Before
> using Micromanager/ImageJ, my TIFF images could be opened in any program. I
> need to be able to open them in programs other than ImageJ so that I can
> analyze the images in MATLAB. If I open each image individually with ImageJ
> and save the files as another filetype, like JPEG, then I can open them in
> any program. However, I am taking many images, so this is too tedious for
> my situation.
>
> Any suggestions would be greatly appreciated.
>
> Thank you,
>
> Hani
>

[Krs5]

Hi Hani,

It also depends which program you use to open your images. Some programs cannot open 16 bit images, only 8 bit. If you can open your images in ImageJ and for example Gimp or Irfanview but not your other program this might be the problem. See what happens if you change the type to 8-bit and save the image as tif (under a different name) and try to open them in you program. If it now works, your program does not handle 16-bit images.

Best wishes

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: 28 March 2012 04:04
To: [hidden email]
Subject: Re: ImageJ Micromanager Tiff images

Hi Hani,


I am taking 16-bit TIFF images using a Micromanager as an ImageJ plugin.
> I've been having a simple problem opening these TIFF images. They open fine
> when opened in ImageJ, but they do not open or they appear black when
> opened in any other program that is capable of taking TIFF images.
>

Chances are that your actual data values are correct-it's just the
visualization that appears all black. Since you have 16-bit images, it is
likely the data is being scaled from 0-65535, when your actual intensity
range is much lower (e.g., for a 12-bit camera, you won't have intensity
values above 4095).

You will want to autoscale your display min/max based on the data before
visualizing it. In the case of MATLAB with the imagesc function, you can
set the bounds explicitly using the clims parameter. For details, see:
http://www.mathworks.com/help/techdoc/ref/imagesc.html

Regards,
Curtis

P.S. You can use Bio-Formats to read Micro-Manager data into MATLAB; see:
   http://loci.wisc.edu/bio-formats/matlab


On Tue, Mar 27, 2012 at 8:49 PM, Hani Mahmoud <[hidden email]> wrote:

> Hello,
>
> I am taking 16-bit TIFF images using a Micromanager as an ImageJ plugin.
> I've been having a simple problem opening these TIFF images. They open fine
> when opened in ImageJ, but they do not open or they appear black when
> opened in any other program that is capable of taking TIFF images. Before
> using Micromanager/ImageJ, my TIFF images could be opened in any program. I
> need to be able to open them in programs other than ImageJ so that I can
> analyze the images in MATLAB. If I open each image individually with ImageJ
> and save the files as another filetype, like JPEG, then I can open them in
> any program. However, I am taking many images, so this is too tedious for
> my situation.
>
> Any suggestions would be greatly appreciated.
>
> Thank you,
>
> Hani
>