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

Tue May 29 17:22:56 BST 2018

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/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20180529/c2b7a812/attachment.html>