[ome-users] Micro Manager 1.22 broken with Bio-Formats 5.8.x

[Sebastien Besson (Staff)]

 Hi Stéphane,

good to hear from you and sorry to hear about this issue. First of all, I assume you meant Micro-Manager 1.4.22 i.e. the current stable version? Also if I understand correctly this is an issue that happens primarily while writing images in file stacks in Micro-manager?

Having briefly discussed this internally, what you described is a puzzling behavior. A couple of technical points:

- the Micro-Manager TIFF writing code is largely independent of the Bio-Formats codebase. The main place where the Bio-Formats API is consumed is the OMEMetadata class [1] for writing image file stacks.
- the list of changes in Bio-Formats 5.8.0 [2]  does not reveal any immediate smoking gun on an API behavioral change which would have caused this
- the API of the Bio-Formats 5.1 JARs shipped with Micro-Manager 1.4.22 is incompatible with the latest Bio-Formats versions. However, the Bio-Formats API has been kept fully backwards compatible since version 5.3.0 and I suspect you would  have flagged this behavior during recent upgrades.

[1] https://github.com/micro-manager/micro-manager/blob/master/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java
[2] http://docs.openmicroscopy.org/bio-formats/5.8.0/about/whats-new.html

It seems the next action is for us to reproduce a minimal failing case via one of the deployments you suggest i.e. either Icy + Micro-Manager 1.4.22 + Bio-Formats 5.8 or ImageJ + Micro-Manager 1.4.22 + Bio-Formats 5.8.

Will anyone from your team or one of your users be present at our Users meeting next week? If so, we could schedule some time and go through this issue. Otherwise, we might have to wait until the week of June 4 and possibly try to arrange a call with you guys so that you can guide us through the workflow.

Best,
Sebastien



________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of Stephane Dallongeville <stephane.dallongeville at pasteur.fr>
Sent: Wednesday, May 23, 2018 6:17:36 PM
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] Micro Manager 1.22 broken with Bio-Formats 5.8.x

Dear Bio-Formats developers,

Since Bio-Formats 5.8.0, the Multi-D acquisition from Micro-Manager
(version 1.22 and probably previous 1.xx) is not working anymore (it
does not output any image).
This happen when we have Bio-Format (5.8.x) and Micro-Manager inside
ImageJ and it also immediately affects Micro-Manager in Icy as
Bio-Formats is embedded inside it.
I observed the 'tags' from acquired TaggedImage are empty, leading to
that issue.. this wasn't happening with Bio-Formats < 5.8.0.
I wonder how Bio-Formats can interact with MM during Multi-D acquisition
but it definitely seems to do something about it.
I hope it can be fixed as our Micro-Manager users cannot use it anymore
now, in the meantime we will probably rollback to older Bio-Formats
version but it would be nice to benefit from last additions of
Bio-formats in Icy ;)

Best,

--
Stephane Dallongeville
Unité d'Analyse d'Images Biologiques
CNRS UMR 3691
Institut Pasteur
25 rue du Dr. Roux
75724 Paris cedex 15 (FRANCE)

Tel: +33 (0)1 45 68 87 01
Fax: +33 (0)1 40 61 33 30

http://www.bioimageanalysis.org/
Bio Image Analysis | Unité d'Analyse d'Images Biologiques ...<http://www.bioimageanalysis.org/>
www.bioimageanalysis.org
The scientific project of the Quantitative Image Analysis (QuIA) unit is to develop image analysis and computer vision tools for the processing and quantification of biological images, with a strong focus on multi-channel temporal 3D sequences.



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