[ome-devel] [IDR Project] Zegami / IDR
William Moore (Staff)
W.Moore at dundee.ac.uk
Mon Jul 4 11:49:46 BST 2016
Hi Damir,
How do you want to name your Wells in the csv file?
If you name Wells like
…
Z01
AA01
AA02
etc.
then you can add these lines to populate_metadata.py to extend the AS_ALPHA by another 26 rows.
AS_ALPHA = [chr(v) for v in range(97, 122 + 1)] # a-z
+ # Support more than 26 rows
+ for v in range(97, 122 + 1):
+ AS_ALPHA.append('a' + chr(v))
WELL_REGEX = re.compile(r'^([a-zA-Z]+)(\d+)$’)
This works for me with my local setup.
I haven’t discussed with the Glencoe authors of the script whether this is the “right” way to fix this, but
please let us know if it works for you?
Cheers,
Will.
On 3 Jul 2016, at 01:15, Damir Sudar <dsudar at lbl.gov<mailto:dsudar at lbl.gov>> wrote:
Hi Eleanor and OME team,
When trying to use the various metadata populate utilities for our project I ran into what I think is a bug:
When the number of rows in a plate exceeds 26 (i.e. beyond row "Z"), the Populate_Metadata.py script (and presumably the underlying functionality that does the actual work) fails with the error:
Traceback (most recent call last):
File "./script", line 130, in <module>
message = populate_metadata(client, conn, scriptParams)
File "./script", line 85, in populate_metadata
ctx = ParsingContext(client, omero_object, "")
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 442, in __init__
self.value_resolver = ValueResolver(self.client, self.target_object)
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 245, in __init__
return self.load_plate()
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 318, in load_plate
self.target_object, wells_by_location, wells_by_id, images_by_id
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 330, in parse_plate
columns = wells_by_location[self.AS_ALPHA[row]]
IndexError: list index out of range
I'm working with high density printed microarray grids of 20 by 35 cell-spots in 8-well plates and I'm abusing the the Screen/Plate/Well functionality by treating each cell spot as a Well, each Array as a Plate, and each of my 8-well plates as a Screen. So far all this works great until this point.
I tried some work-arounds such as changing the naming scheme of Rows and Columns (as Dataset_To_Plate.py allows) so that the Rows get the numbers and the Columns get the letters but alas, that fails with the same error so the max number of rows limit of 26 appears to be pretty deeply embedded somewhere.
So I looked at the piece of code (populate_metadata.py) where this fails and found two issues:
1) the TODO note: which explains why my work-around failed
# TODO: This should use the PlateNamingConvention. We're assuming rows
# as alpha and columns as numeric.
2) the AS_ALPHA macro evaluates incorrectly when the row is interpreted as a single letter: which is why anything past "Z" fails
Any chance someone smarter than I could have a look and fix?
Thanks,
- Damir
On 6/27/2016 2:03 PM, Eleanor Williams wrote:
Hi Damir
To convert the omero tables to key-value pairs annotations we are again using the CLI metadata populate script along with a yaml-format configuration file to specify which columns we want to take from the omero tables and put into Key-Value Annotations.
This component of the metadata functionality is still in the development stage and so to use it you need to:
1. use the latest version of omero (5.2.4) and
2. then run as
OMERO_DEV_PLUGINS=1 bin/omero metadata populate --context bulkmap --cfg bulkmap-config.yml Screen:n
where n is the screen number in omero.
An example config file for one of our screens is here
<https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml><https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml>https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml
You can see I have just picked out some of the columns from theannotation.csv<https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-annotation.csv> file, in this case ones that I thought IDR users might use as search terms, and I have specified URLs for some. You can also change the 'display name' of the column using the ' clientname' tag and create URLs using the 'clientvalue' tag.
Let us know if you have any problems running this, or suggestions for improvement.
Best regards
Eleanor
On 27/06/2016 03:04, Damir Sudar wrote:
Hi Eleanor and Josh,
I'm learning a lot from your work on putting the IDR together and I'm applying it for our image repository for our LINCS project (http://www.lincsproject.org/centers/data-and-signature-generating-centers/oregon-u/) that hopefully will go live in a few months. We're also looking at Zegami as a possible way to provide visualizations of that data (Great demo, Roger!! and thanks for the code for that).
I've gotten as far as putting my metadata into a a format that can be used to generate the omero tables using the Populate Metadata script. But I couldn't find how you guys then populate the Key-Value Annotations. It appears to be a subset of what's in the Tables. Do you have some magic scripts for that and are those available?
Cheers,
- Damir
On 6/16/2016 2:21 AM, Eleanor Williams wrote:
Hi Steve and Roger
I think idr0002-heriche-condensation would be a good screen to start with. It is relatively small at 12 plates and has good annotation with control, quality control and phenotype values. It can be found here http://idr-demo.openmicroscopy.org/webclient/?show=screen-102.
I am doing a bit of a stock-take of the annotation files I've produced so far and will be changing a few aspects over the next few weeks, mainly to include more of the information that is currently held in the study files. For example I'd like to get more of the sample attributes such as species and cell line into the annotation.csv file, and then into the omero tables and Map Annotations. Sample attributes for screens were originally recorded in the study file because it didn't vary per screen, but now that we are also looking at non-screen data where this might vary it makes sense to always have it visible with the images. Also we haven't got as far as exposing much of the study information in omero yet.
I would really like to work with you to understand how you are going to use the experimental and analytic annotations and how we can help in providing the metadata you need and in the most usable format. For example would it be useful if I indicate what is sample attribute information in the annotation.csv file by using something like a constistent header format e.g. Characterisics [Organism], Characteristics [Cell Line], Characteristics [Organism Part] etc, or is this not really necessary for your purposes and 'Organism', 'Cell Line' column headings would be enough?
Finally, it was Balaji Ramalingam<https://www.openmicroscopy.org/site/about/development-teams/jason/balaji.png/view> that you were talking to about streaming the thumbnails. I'm sure he would be happy to discuss this further with you.
Best regards
Eleanor
On 15/06/2016 20:59, Josh Moore wrote:
Forwarding this to the mailing list so that anyone who had expressed
interested in http://zegami.com/ at this year's users' meeting can
follow along.
Cheers,
~Josh
P.S. If you weren't able to attend #OME2016, a recap is now up on the
blog http://blog.openmicroscopy.org/community/2016/06/15/user-meeting/
---------- Forwarded message ----------
From: Stephen Taylor <stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk>
Date: Tue, Jun 14, 2016 at 8:17 AM
Subject: Re: [IDR Project] Zegami / IDR
Cc: Roger Noble <roger at zegami.com><mailto:roger at zegami.com>
Hi,
I’ve been look at a few examples from the link Josh sent to me and
there are quite a lot! What would be a good data set to get import
into Zegami from IDR? I am thinking a set that has decent metadata
and a study that people are more familiar with that would make an
interesting use case.
Kind regards,
Steve
From: Stephen Taylor
Sent: 10 June 2016 14:25
Cc: Roger Noble <roger at zegami.com><mailto:roger at zegami.com>; 'e.x.williams at dundee.ac.uk<mailto:e.x.williams at dundee.ac.uk>'
<e.x.williams at dundee.ac.uk><mailto:e.x.williams at dundee.ac.uk>
Subject: RE: [IDR Project] Zegami / IDR
Hi all,
I am interested generally in getting data in and out of OMERO from
both internal and external. Over a WAN the images are less of an issue
since they are streamed on demand but large metadata on the other hand
can get out of hand since it all has to be loaded completely into
Zegami’s database.
Currently I do “OMERO project” to “Zegami collection” using a Zegami
export script (modified version of the OMERO batch export script).
This takes a project or selection of images from OMERO and produces
thumbnails and data in tab delimited Zegami format and then I manually
import that into Zegami for processing. The OMERO id is preserved so I
can link to the original image in OMERO using the OMERO web client. I
only export certain metadata currently (filenames and OMERO tags) and
my plan is to make this more comprehensive and allow MapAnnotations
and Tables to be exported using this mechanism as well. I need to find
out more how to query these data types. Since we have internal
projects at Oxford that need this I’d like to finish this and make
that plugin freely available for other OMERO users to publish their
data in Zegami.
Longer term for IDR/Zegami
One of your team (apologies I didn’t get his name but he was doing
OMERO/ImageJ in the Unconference session) suggested we just stream in
the thumbnail and just have 1 level (i.e. no zoom) and when you want
to see the image just open it up in OMERO. This would not be as nice
to use but may be sufficient for HCS and would allow you to use
Zegami’s facet based query engine and would be probably little (no?)
work for you guys. We need to test this to see what it looks like and
it assumes OMERO can supply a unique thumbnail URL for each image and
that the metadata will provide a primary key so that we can get to
this image via a thumbnail id. To get at the metadata Josh and Eleanor
said they were thinking of making the CSV downloadable for a
collection, which could be loaded into Zegami on the fly (we have
instances where we dynamically load metadata via URL already).
However, major caveat is on how well this would perform over a WAN
with a large amount of data.
BTW we have developer docs for Zegami for those interested at:
https://support.zegami.com/hc/en-us/categories/200350657-Developers
and would welcome feedback.
Kind regards and thanks,
Steve
From: Jason Swedlow (Staff) [mailto:j.r.swedlow at dundee.ac.uk]
Sent: 08 June 2016 13:09
Cc: Eleanor Williams (Staff) <e.x.williams at dundee.ac.uk><mailto:e.x.williams at dundee.ac.uk>
Subject: Re: [IDR Project] Zegami / IDR
Hi Josh et al—
My two cents— can we consider this use case from an external users’
perspective, mindful that distribution of such a solution would
definitely cause us to consider how we ship thumbnails, handle
straws, etc.
Cheers,
Jason
On Wed, Jun 8, 2016 at 1:31 PM, Josh Moore <josh at glencoesoftware.com><mailto:josh at glencoesoftware.com> wrote:
Stephen,
On Wed, Jun 8, 2016 at 9:52 AM, Stephen Taylor
<stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk> wrote:
Hi Josh,
Yes! What would be the best way of bulk downloading the thumbnails for a screen or plate
Interesting question. Guess the reverse question is: do you want to do
this as an external user or as if you had access to the OMERO?
( I notice the "Run Script" button isn't active ).
Correct. This server is stripped down in several ways as a public resource.
~J.
Kind regards,
Steve
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: 08 June 2016 08:07
To: Stephen Taylor <stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk>
Cc: Eleanor Williams <exwilliams at dundee.ac.uk><mailto:exwilliams at dundee.ac.uk>;
e.x.williams at dundee.ac.uk<mailto:e.x.williams at dundee.ac.uk>; j.a.moore at dundee.ac.uk<mailto:j.a.moore at dundee.ac.uk>
Subject: Re: Zegami / IDR
Hi Stephen,
On Wed, Jun 8, 2016 at 8:40 AM, Stephen Taylor
<stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk> wrote:
Hi Eleanor,
Thanks very useful. Is the web site publically available?
You mean http://idr-demo.openmicroscopy.org/webclient ?
Cheers,
~Josh
Kind regards and thanks,
Steve
From: Eleanor Williams [mailto:exwilliams at dundee.ac.uk]
Sent: 07 June 2016 11:09
To: Stephen Taylor <stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk>;
e.x.williams at dundee.ac.uk<mailto:e.x.williams at dundee.ac.uk>; j.a.moore at dundee.ac.uk<mailto:j.a.moore at dundee.ac.uk>
Subject: Re: Zegami / IDR
Hi Stephen
Here is a link to our workshop presentation but it describes how to
get the data into omero rather than out.
http://downloads.openmicroscopy.org/presentations/2016/Users-Meeting/Workshops/Metadata-at-Scale.pdf
We will be adding the annotation.csv files as attachments to each
screen over the next couple of weeks.
Let us know if you have any more questions.
Best regards
Eleanor
On 07/06/2016 10:41, Stephen Taylor wrote:
Hi Eleanor and Josh,
Great to meet you both at the OME meeting last week.
I'd be interested in trying get some data into Zegami from IDR. I
missed your Unmeeting (ironically I was demoing Zegami) where I think
you went into some of the technical details. Can you send me the link
to your presentation please?
Kind regards and thanks,
Steve
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--
Eleanor Williams PhD
Data Annotator/Software Engineer
Centre for Gene Regulation and Expression
University of Dundee, UK
The University of Dundee is a registered Scottish Charity, No: SC015096
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Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>
http://biosciences.lbl.gov/profiles/damir-sudar-2/
Visiting Scientist, Oregon Health & Science University
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--
Eleanor Williams PhD
Data Annotator/Software Engineer
Centre for Gene Regulation and Expression
University of Dundee, UK
The University of Dundee is a registered Scottish Charity, No: SC015096
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ome-devel mailing list
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--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>
http://biosciences.lbl.gov/profiles/damir-sudar-2/
Visiting Scientist, Oregon Health & Science University
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