<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Hi Anatole</div>
<div><br>
</div>
<div>It'd be great to hear of your experiences with Neo4J, especially with regards to its performance with very large numbers of samples and features. As you probably already know OMERO.biobank [1] also uses it, though for a different use case, and it's one
of the many things we're considering as an addition to OMERO.</div>
<div><br>
</div>
<div>Let's talk in Paris, if not before!</div>
<div><br>
</div>
<div>Simon</div>
<div><br>
</div>
<div>[1] <a href="http://www.openmicroscopy.org/site/support/partner/omero.biobank/">http://www.openmicroscopy.org/site/support/partner/omero.biobank/</a></div>
<br>
<div>
<div>On 9 May 2014, at 15:43, Anatole Chessel <<a href="mailto:ac744@cam.ac.uk">ac744@cam.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000"><br>
Hi all,<br>
<br>
I have been following the discussion on OMERO.features as it does fall quite quite close to issues we have and things we are doing as well, even though I did not participate. I thought I would chime in to say what we are up to in this domain; we'll be in
Paris for the OME user meeting likely with a poster and happy to discuss...<br>
<br>
We are doing yeast genome wide HT/HC microscopy studies and up to now we've used a SQL database to store cell-wise feature extracted from images (as we are just one lab with coherent experiments -but a lot of data- it sounded like a good idea). We are currently
looking into Neo4J as a more flexible solution, and working on a HTML5 front-end enabling visualisation and mining to the wider audience of experimental biologist. Although I haven't used it that deeply -yet-, I quite like neo4j as it does keep some structure
to the data while not being as rigid as sql. And I guess we went the opposite way and stored all relevant information in the SQL/Neo4J DB, with the link with OMERO being provided by having the IDs of omero objects stored somewhere.<br>
<br>
Again, happy to talk in Paris about those things, which are indeed a common pain in the community...<br>
<br>
Cheers<br>
Anatole<br>
<br>
<br>
<div class="moz-cite-prefix">On 08/05/2014 14:40, Simon Li wrote:<br>
</div>
<blockquote cite="mid:324E93CC-3390-4A86-BBE8-A933C3D001D9@dundee.ac.uk" type="cite">
<div>
<div>Hi all</div>
<div><br>
</div>
<div>I've started a Github repository for trying out some OMERO.features ideas based on what I mentioned in the last email:</div>
<div><a moz-do-not-send="true" href="https://github.com/manics/omero-features">https://github.com/manics/omero-features</a></div>
<div><br>
</div>
<div>There's not a great deal in there at the moment. It's just saving features into a local HDF5 file using Pytables, and example.py creates a table similar to that used by Pyslid (OMERO.searcher). timings.txt shows some rough run-times. Key-value row pairs
are mapped to table columns, however this means each row has to have the same keys. There's no simple way to have a key-value map per column, for now I'm just storing multiple features in one column.</div>
<div><br>
</div>
<div>This is easily convertible to OMERO.tables, columns could be labelled using OMERO annotations (in 5.1 there's a new MapAnnotation), though it effectively means each group of features is stored separately and thus would need to be queried separately. Alternatively
an auxiliary table could be used to store the per-column key-value pairs, similar to how column descriptions are currently stored in OMERO.tables.</div>
<div><br>
</div>
<div>A major limitation is that database joins between OMERO and a feature-table aren't practical. For example, if each feature row is labelled with an image ID, and you want to select a subset of rows using an OMERO query, you have to pass a list of image
IDs to the Pytables query function which from my initial testing is very limited in the number of parameters it'll handle (I get a stack overflow if too many image IDs are passed).</div>
<div><br>
</div>
<div>In practice this means you'd either need the feature table to contain any metadata necessary for selecting rows (e.g. dataset ID, experiment parameters, annotations) even if this means duplicating information held in OMERO, or split the query up (very
inefficient). This is probably fine for people dealing with features in bulk where you might download all features for a screen for offline processing, not so good for real-time searching such as OMERO.searcher where you'd either need to store everything you
need for pre-filtering search results in the table, or read all features and do the filtering afterwards.</div>
<div><br>
</div>
<div>Probably OK as far as developing the API is concerned, but longer term it suggests we need some other storage mechanism. Some of you will remember Joaquin Correa from Paris last year. He's currently working on his own feature storage implementation at
LBL, so potentially this is something we could look at for OMERO, and of course there are many other possibilities.</div>
<div><br>
</div>
<div>Simon</div>
</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div>
<div>On 24 Apr 2014, at 12:57, Lee Kamentsky <<a moz-do-not-send="true" href="mailto:leek@broadinstitute.org">leek@broadinstitute.org</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hi all,<br>
<div class="gmail_extra">Just chiming in, since we were mentioned...<br>
<br>
<div class="gmail_quote">On Wed, Apr 23, 2014 at 5:10 PM, Simon Li <span dir="ltr">
<<a moz-do-not-send="true" href="mailto:s.p.li@dundee.ac.uk" target="_blank">s.p.li@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all<br>
<br>
Now that OMERO 5.0 is out of the way, and OMERO.searcher and WND-CHRM are either released or very close to release, I think it's time to restart our OMERO.features discussions.<br>
<br>
We got as far as the idea of a 2D table with any number of key-value pairs on each column and row, so for example each row could be as simple as (OmeroType: Image, OmeroId: 123), or in the case of features which are a function of multiple images or channels
(OmeroType: Image, OmeroId: 123, Channel1: 0, Channel2: 3), etc. Columns could for example be (FeatureFamily: WndCharm, Feature: Zernike). Each table cell could either be a scalar or array. Retrieving features could be done by providing key-value pairs to
be matched.<br>
<br>
All of this is still up for discussion, especially since the implementation of this interface could be challenging and there's some redundancy/ambiguity. Just to be clear, the above is a conceptual description of how the API would appear to users, the actual
back-end could be completely different.<br>
<br>
Lee Kamentsky gave us a use case just before Christmas [1], Chris Coletta and Ivan Cao-berg are planning to summarise how they see WND-CHARM and OMERO.searcher fitting in. I know a few other people are interested in this discussion, so feel free to respond
here or in the forums.<br>
</blockquote>
<div><br>
</div>
<div>For us, it's important to link features to regions of interest, specifically segmentations of whole cells and cellular compartments. The other issues have to do with scalability and the efficiency of retrieving large data sets either by selecting a few
features for a large number of images (e.g. up to on the order of 1,000,000 images and 1,000 entries per feature per image) or by selecting many or all features associated with a subset of the regions of interest.</div>
<div><br>
</div>
<div>We are also interested in recording tracking data. What's needed here is the ability to record a link between the region of interest in one frame of a time-series stack with a region of interest in a later frame and you need the flexibility of a many-many
relationship to represent cell division and potentially merging. I'm fairly confident that you could encode that sort of thing in a 2-D table which had columns referencing both ROIs.</div>
<div><br>
</div>
<div>Finally, we try to capture enough information about the analysis to make it reproducible - things like the pipeline used for the analysis, the GIT hash of the software used to run the analysis and of each image analyzed. I think all of that is easily captured,
though, in the tables and I doubt we need any explicit functionality devoted to that. It might be nice to be able to annotate the table itself with attributes in order to document the linking of the analysis results to the experimental protocol, but the linking
could be documented using columns in an experiment-wide table.</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
A few of us are planning to meet up at the OME Paris meeting- if you're interested drop me an email.<br>
<br>
Thanks<br>
<br>
Simon<br>
<br>
[1] <a moz-do-not-send="true" href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2013-November/002573.html" target="_blank">
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2013-November/002573.html</a><br>
<br>
<br>
On 7 Nov 2013, at 14:20, Simon Li <<a moz-do-not-send="true" href="mailto:s.p.li@dundee.ac.uk">s.p.li@dundee.ac.uk</a>> wrote:<br>
<br>
> Some notes from our meeting yesterday:<br>
> <a moz-do-not-send="true" href="http://www.openmicroscopy.org/site/community/minutes/minigroup/omero-features-meetings/2013-11-06-omero-features-google-hangout" target="_blank">
http://www.openmicroscopy.org/site/community/minutes/minigroup/omero-features-meetings/2013-11-06-omero-features-google-hangout</a><br>
><br>
> Summary:<br>
> We're thinking of representing features as a 2D array, with metadata stored as key-value maps attached to the array, or individual columns or rows. These keys could describe things such as the feature name (column), sample metadata (row), algorithm parameters,
calculation pipelines, etc.<br>
><br>
> This should work as an OMERO API- in order to retrieve features you'd pass in a set of key-value pairs, for instance to specify which features you want and which images/ROIs etc, and OMERO would handle the logic and return the feature table(s) matching those
parameters. Since everyone has different requirements the keys could be anything, however we're trying to define a small set of standard keys- any suggestions are very welcome.<br>
><br>
> Outside of OMERO we still need a format for transporting features, so we're thinking some form of HDF5.<br>
><br>
> Simon<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
> _______________________________________________<br>
> ome-devel mailing list<br>
> <a moz-do-not-send="true" href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>
> <a moz-do-not-send="true" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
_______________________________________________<br>
ome-devel mailing list<br>
<a moz-do-not-send="true" href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a moz-do-not-send="true" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset> <br>
<pre wrap="">_______________________________________________
ome-devel mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a>
</pre>
<br>
<pre class="moz-signature" cols="72">--
Anatole Chessel, PhD
Research associate
University of Cambridge
Tennis Court Road, Cambridge CB2 1PD
tel: +44 (0)1223 334065</pre>
</blockquote>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br>
</blockquote>
</div>
<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>