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Hi Sebastien,<br>
<br>
Thanks and sorry for the late reply, yeah i meant Micro-Manager
1.4.22 ;)<br>
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.<br>
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...<br>
Still i have no real idea about how Bio-formats 5.8.0 (or above) can
lead to that issue.<br>
<br>
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.<br>
<br>
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 :)<br>
<br>
Best,<br>
<br>
- Stephane<br>
<br>
<br>
<div class="moz-cite-prefix">Le 24/05/2018 à 22:39, Sebastien Besson
(Staff) a écrit :<br>
</div>
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<div> Hi Stéphane,<br>
<br>
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?<br>
<br>
Having briefly discussed this internally, what you described
is a puzzling behavior. A couple of technical points:<br>
<br>
- 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.<br>
- 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<br>
- 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.</div>
<div><br>
</div>
<div>[1]
<a class="moz-txt-link-freetext" href="https://github.com/micro-manager/micro-manager/blob/master/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java">https://github.com/micro-manager/micro-manager/blob/master/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java</a><br>
[2]
<a class="moz-txt-link-freetext" href="http://docs.openmicroscopy.org/bio-formats/5.8.0/about/whats-new.html">http://docs.openmicroscopy.org/bio-formats/5.8.0/about/whats-new.html</a><br>
</div>
<div><br>
</div>
<div>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.</div>
<div><br>
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.<br>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien<br>
<br>
</div>
<br>
</div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
ome-users
<a class="moz-txt-link-rfc2396E" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><ome-users-bounces@lists.openmicroscopy.org.uk></a> on
behalf of Stephane Dallongeville
<a class="moz-txt-link-rfc2396E" href="mailto:stephane.dallongeville@pasteur.fr"><stephane.dallongeville@pasteur.fr></a><br>
<b>Sent:</b> Wednesday, May 23, 2018 6:17:36 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b> [ome-users] Micro Manager 1.22 broken with
Bio-Formats 5.8.x</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span
style="font-size:11pt;">
<div class="PlainText">Dear Bio-Formats developers,<br>
<br>
Since Bio-Formats 5.8.0, the Multi-D acquisition from
Micro-Manager <br>
(version 1.22 and probably previous 1.xx) is not working
anymore (it <br>
does not output any image).<br>
This happen when we have Bio-Format (5.8.x) and
Micro-Manager inside <br>
ImageJ and it also immediately affects Micro-Manager in
Icy as <br>
Bio-Formats is embedded inside it.<br>
I observed the 'tags' from acquired TaggedImage are
empty, leading to <br>
that issue.. this wasn't happening with Bio-Formats <
5.8.0.<br>
I wonder how Bio-Formats can interact with MM during
Multi-D acquisition <br>
but it definitely seems to do something about it.<br>
I hope it can be fixed as our Micro-Manager users cannot
use it anymore <br>
now, in the meantime we will probably rollback to older
Bio-Formats <br>
version but it would be nice to benefit from last
additions of <br>
Bio-formats in Icy ;)<br>
<br>
Best,<br>
<br>
-- <br>
Stephane Dallongeville<br>
Unité d'Analyse d'Images Biologiques<br>
CNRS UMR 3691<br>
Institut Pasteur<br>
25 rue du Dr. Roux<br>
75724 Paris cedex 15 (FRANCE)<br>
<br>
Tel: +33 (0)1 45 68 87 01<br>
Fax: +33 (0)1 40 61 33 30<br>
<br>
<a href="http://www.bioimageanalysis.org/"
id="LPlnk723589" class="OWAAutoLink"
previewremoved="true" moz-do-not-send="true">http://www.bioimageanalysis.org/</a></div>
</span></font></div>
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