Importing an image into Micromanager 2.0?

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Importing an image into Micromanager 2.0?

Karl Bellve-3


Trying to import a synthetic image data set into Micromanager 2.0 to test KNIME detecting nuclei in images from Micromanager.

Creating a OME Tiff in FIJI and importing that doesn't work but it could be an incorrect setting.

Any tricks?


Cheers Karl

Karl Bellvé
Biomedical Imaging Group
Molecular Medicine
University of Massachusetts Medical School




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Re: Importing an image into Micromanager 2.0?

Nico Stuurman-2
Hi Karl,

On 10/12/17 7:39 AM, Karl Bellve wrote:
> Trying to import a synthetic image data set into Micromanager 2.0 to
> test KNIME detecting nuclei in images from Micromanager.
>
> Creating a OME Tiff in FIJI and importing that doesn't work but it
> could be an incorrect setting.
>
> Any tricks?

That is a great question, and unfortunately, I have no good answers.  MM
is indeed very picky about Metadata, and it is not easily convinced to
read in other TIFF files.  It would be nice to make something less
picky, but if I would need to deal with your issue right now, I may look
into creating a device adapter that reads TIFFs from disk and behaves as
a camera (in fact, such a thing may already exist).

Best,


Nico


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Importing an image into Micromanager 2.0?

Karl Bellve-3
Forgot to reply all...


On Mon, Oct 16, 2017, 5:34 PM Nico Stuurman <[hidden email]> wrote:
Hi Karl,

On 10/12/17 7:39 AM, Karl Bellve wrote:
> Trying to import a synthetic image data set into Micromanager 2.0 to
> test KNIME detecting nuclei in images from Micromanager.
>
> Creating a OME Tiff in FIJI and importing that doesn't work but it
> could be an incorrect setting.
>
> Any tricks?

That is a great question, and unfortunately, I have no good answers.  MM
is indeed very picky about Metadata, and it is not easily convinced to
read in other TIFF files.  It would be nice to make something less
picky, but if I would need to deal with your issue right now, I may look
into creating a device adapter that reads TIFFs from disk and behaves as
a camera (in fact, such a thing may already exist).

Best,


Nico

Hi Nico,

What I think I might do is modify the demo camera to include a 4th option to load an image from file, and every time the camera is snapped, the next image is loaded. I took a look at the demo camera code today and I think it is a fesiable approach. 


Cheers Karl


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Re: Importing an image into Micromanager 2.0?

Kyle Douglass

Hi Karl,


What I think I might do is modify the demo camera to include a 4th option to load an image from file, and every time the camera is snapped, the next image is loaded. I took a look at the demo camera code today and I think it is a fesiable approach. 



Marcel Stefko, a masters student from our lab, developed a MM 2.0 plugin that reads images from a .tif stack and feeds them through the Live window, effectively simulating an acquisition. It's a bit of a dirty hack since it's implemented at the level of the processing pipeline, i.e. not a device adapter, but you may still find it useful.

https://github.com/LEB-EPFL/ImageInjector

I'm still moving Marcel's work into a consolidated place on Github; until I do, the .jar file is in the Releases section of the original repo: https://github.com/MStefko/ImageInjectorPlugin

A brief description on how to use it may be found in the README and here: http://alica.readthedocs.io/en/latest/simulation.html

We decided against directly modifying the demo camera since it runs on a pretty large code base...

Cheers,
Kyle

-- 
Kyle M. Douglass, PhD
Post-doctoral researcher
The Laboratory of Experimental Biophysics
EPFL, Lausanne, Switzerland
http://kmdouglass.github.io
http://leb.epfl.ch

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