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

[Melissa Linkert]

Hi Stéphane,

Thank you for the additional information.  I can reproduce the problem
exactly as you describe when installing Bio-Formats 5.8.2 into a new
installation of Micro-Manager 1.4.22 and attempting a Multi-D
acquisition.

The problem is that Bio-Formats 5.8.0 introduced a dependency upon
org.json, which conflicts with the version of org.json used by
Micro-Manager.  The details are recorded on this Trello card:

https://trello.com/c/9IuVhL0w/30-orgjson-dependency-conflicts-with-orgjson-checked-into-micro-manager-repository

We are currently evaluating the best solution, and will update the
card as we make progress.

Regards,
-Melissa

On Tue, May 29, 2018 at 11:22 AM, Stephane Dallongeville
<stephane.dallongeville at pasteur.fr> wrote:
> Hi Sebastien,
>
> Thanks and sorry for the late reply, yeah i meant Micro-Manager 1.4.22 ;)
> I dunno exactly where happen but the bug but it's easy to reproduce : just
> use the Multi-D acquisition in Micro-Manager and it will happen.
> In Micro-Manager the error happen silently so you don't see any error
> messages but you also don't get any image as a result. In the Icy plugin we
> have an image analyser / processor so i could saw that the 'tags' field from
> the TaggedImage during Multi-D acquisition is empty. These tags contains all
> the metadata (and i guess there is where Micro-Manager can have some
> interaction with Bio-Formats) and are important so no surprise the result
> image don't show when they are empty...
> Still i have no real idea about how Bio-formats 5.8.0 (or above) can lead to
> that issue.
>
> I didn't realized Micro-Manager was using formats-api-5.1.1 and
> formats-common-5.1.1 packages so putting the whole Bio-Formats 5.8.0 in the
> same folder could eventually bring some incompatibilities. Still version BF
> 5.7.3 does not hurt at all while version 5.8.0 break it so i think it's
> definitely due to some recent changes.
>
> Unfortunately I won't be present at the next OME Annual Users Meeting (it
> was simpler when they were at Pasteur Institute in Paris ^^) but we are not
> in a hurry (in the meantime our users are using Bio-Formats 5.7.3) so that
> can wait a bit :)
>
> Best,
>
> - Stephane
>
>
>
> Le 24/05/2018 à 22:39, Sebastien Besson (Staff) a écrit :
>
>  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/
>
>
>
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