Running Micro-Manager in FIJI

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Running Micro-Manager in FIJI

PEARSON Matthew
Hi all,

I have moved what i think are all the relevant Micro-Manager folders/files into my FIJI installation so i can run MM from FIJI instead of IJ to access certain plugins only in FIJI.  The only issue i'm having is when pressing acquire no acquisition window is created and when set to save to disk, it creates the folder for the image but no image is put in.  I can press live, snap and album and this opens the image window.  Does anyone know what might cause this to happen, i have a feeling maybe i've not moved a relevant folder/file from the Micro-Manager installation.  Its MM 1.4 nightly build 13062018.

Thanks,

Matt


--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU





The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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Re: Running Micro-Manager in FIJI

Kyle Douglass-2
Hi Matt,

On Thu, Jun 14, 2018 at 12:44 PM, PEARSON Matthew <[hidden email]> wrote:

I have moved what i think are all the relevant Micro-Manager folders/files into my FIJI installation so i can run MM from FIJI instead of IJ to access certain plugins only in FIJI.  The only issue i'm having is when pressing acquire no acquisition window is created and when set to save to disk, it creates the folder for the image but no image is put in.  I can press live, snap and album and this opens the image window.  Does anyone know what might cause this to happen, i have a feeling maybe i've not moved a relevant folder/file from the Micro-Manager installation.  Its MM 1.4 nightly build 13062018.


Here are just a few thoughts that might help you troubleshoot this problem:

1. Have you checked the CoreLogs for any helpful error messages? On Windows, these are usually stored in C:\Program Files\Micro-Manager\CoreLogs (change the first part to point to your MM folder). You can also make the logging more verbose for debugging. In the GUI, you would navigate to Tools > Options... and then check "Enable debug logging".

2. How new is your Fiji installation? There have been quite a lot of changes to Fiji lately; it now ships with a version of ImageJ and numerous other .jar libraries that are much newer than the equivalents that Micro-Manager uses. (I myself am finding it a bit difficult to keep our lab's own Fiji plugins up-to-date with all the changes, but I understand that they ultimately make it easier on the end-user.) Since Fiji ships with so many libraries that are fundamental to its use, it's likely that you could have a version conflict caused by having two versions of the same library in your Fiji folder. The best way to diagnose this, I think, is to check the core logs for references to any Java packages that could be throwing errors and then search your Fiji directory for duplicates of the library.

3. Minor version increments of key libraries in the new Fiji ecosystem seem (at least in my own experience) to occasionally be backwards incompatible. It's possible that you copied a Micro-Manager library that is incompatible with the other libraries in Fiji. You might want to check anything related to imglib2 in particular since I have recently encountered broken builds when the minor version number of this library is incremented.

I hope this helps!
Kyle


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Re: Running Micro-Manager in FIJI

Sebastien Besson (Staff)

Hi everyone,


following up on this thread as we investigated this problem with Matt yesterday:

- as suggested by Kyle in his previous answer, the problem is indeed a library version conflict and more precisely a conflict between the JSON library which is now shipped as a dependency of Bio-Formats and the one in the Micro-Manager source code
- as a workaround in Fiji, removing the json-20090211.jar which is under the jars/ folder of the Fiji distribution seems to suffice to address  this issue

For those interested in more details, this issue has been brought to our attention by Stephane Dallongeville on the OME mailing lists [1]. The core issue is that Bio-Formats started consuming the official JSON library in its version 5.8.0 for reading some new formats. While adding the upstream library is all works fine in theory, Micro-Manager embeds its own copy of of an older version of this library with the same package name within the source code. Chris Weisiger had started the work to upgrade it to a more recent version but this turned into a larger body of work and was postponed [2].

While the workaround mentioned above works (on Fiji), we are investigating how to mitigate this issue in the mid-term on the OME side. Thoughts from the Micro-Manager team on how to minimize the impact are obviously welcome.

Best,

Sebastien


[1] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2018-June/007063.html

[2] https://github.com/micro-manager/micro-manager/commit/59547e7ab6de7d04e5d21c9f83f883e9439d3d9f#diff-ad11b13f4bc065ba4f55ae39b2130974



On 15 Jun 2018, at 07:21, Kyle Douglass <[hidden email]> wrote:

Hi Matt,

On Thu, Jun 14, 2018 at 12:44 PM, PEARSON Matthew <[hidden email]> wrote:

I have moved what i think are all the relevant Micro-Manager folders/files into my FIJI installation so i can run MM from FIJI instead of IJ to access certain plugins only in FIJI.  The only issue i'm having is when pressing acquire no acquisition window is created and when set to save to disk, it creates the folder for the image but no image is put in.  I can press live, snap and album and this opens the image window.  Does anyone know what might cause this to happen, i have a feeling maybe i've not moved a relevant folder/file from the Micro-Manager installation.  Its MM 1.4 nightly build 13062018.


Here are just a few thoughts that might help you troubleshoot this problem:

1. Have you checked the CoreLogs for any helpful error messages? On Windows, these are usually stored in C:\Program Files\Micro-Manager\CoreLogs (change the first part to point to your MM folder). You can also make the logging more verbose for debugging. In the GUI, you would navigate to Tools > Options... and then check "Enable debug logging".

2. How new is your Fiji installation? There have been quite a lot of changes to Fiji lately; it now ships with a version of ImageJ and numerous other .jar libraries that are much newer than the equivalents that Micro-Manager uses. (I myself am finding it a bit difficult to keep our lab's own Fiji plugins up-to-date with all the changes, but I understand that they ultimately make it easier on the end-user.) Since Fiji ships with so many libraries that are fundamental to its use, it's likely that you could have a version conflict caused by having two versions of the same library in your Fiji folder. The best way to diagnose this, I think, is to check the core logs for references to any Java packages that could be throwing errors and then search your Fiji directory for duplicates of the library.

3. Minor version increments of key libraries in the new Fiji ecosystem seem (at least in my own experience) to occasionally be backwards incompatible. It's possible that you copied a Micro-Manager library that is incompatible with the other libraries in Fiji. You might want to check anything related to imglib2 in particular since I have recently encountered broken builds when the minor version number of this library is incremented.

I hope this helps!
Kyle

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