[ome-devel] Fwd: [IDR Project] Zegami / IDR
Damir Sudar
dsudar at lbl.gov
Tue Jul 12 04:27:24 BST 2016
Thanks Simon,
I'm using the tools in our daily workflow now and will have more
feedback. But so far, it's all meeting my needs.
For my need to delete the previous bulkmap annotations I kludged up a a
few lines of shell script that work. It's pretty ugly but may indicate
what's needed:
> # identify Screen ID and delete old bulk_annotation
> s_id=$(omero hql --style=plain --all -q --limit=10 "select s
> from Screen s where s.name = '$arg' " | cut -f3 -d, )
> OA=$(omero hql -q --all --style plain --limit 1 "select
> '/FileAnnotation:'||f.id from ScreenAnnotationLink l, FileAnnotation f
> join l.child where l.child = f and l.parent.id = '$s_id' and
> f.description = 'bulk_annotations' " | cut -f2 -d,)
> if [ "$OA" == "" ]; then omero delete $OA; fi
Am I correct in assuming that deleting the bulk-annotations
FileAnnotation deletes the OMERO.table associated with that Screen and
makes everything "virgin" again?
Thanks,
- Damir
On 7/8/2016 12:21 PM, Simon Li wrote:
>
> Hi Damir
>
> Thanks for your feedback! Improving the map annotation processing
> (which may include removing duplicates, deleting, merging and
> replacing) is definitely on our todo list, along with tools for
> viewing them, keep an eye on the mailing lists for updates.
>
> If you've got any other suggestions, big or small, let us know. We
> want to release the metadata work as a production quality tool, so any
> external feedback is especially welcome.
>
> Simon
>
> On 8 Jul 2016 19:54, "Damir Sudar" <dsudar at lbl.gov
> <mailto:dsudar at lbl.gov>> wrote:
>
> Hi Eleanor and team,
>
> I've been having a lot of fun with all the tools you all have
> developed in the IDR context. Most of them work extremely well as
> is for my purpose. With the CLI metadata tools my whole workflow
> is quite smooth. I look forward to a bit more documentation but
> with built-in help and sometimes a look at the source, I figured
> out most of the functionality. Since I'm still in development
> mode, the "--context deletemap" option is extremely useful. One
> thing I'm missing is an option such as "--context
> delete_bulk_annotations" to conveniently get rid of the previous
> version.
>
> Per my earlier message, I ran into an issue with plates with more
> than 26 rows but Will Moore's partial patch got me over that issue
> for the time being.
>
> 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
>>
>>
>> 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 inhttp://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
>>>>> bloghttp://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 meanhttp://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
>>>>> _______________________________________________
>>>>> ome-devel mailing list
>>>>> ome-devel at lists.openmicroscopy.org.uk
>>>>> <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>>
>>>> --
>>>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> ome-devel mailing list
>>>> ome-devel at lists.openmicroscopy.org.uk
>>>> <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>
>>> --
>>> Damir Sudar - Affiliate Scientist
>>> Lawrence Berkeley Natl Laboratory / MBIB
>>> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
>>> T:510/486-5346 <tel:510%2F486-5346> - F:510/486-5586 <tel:510%2F486-5586> - E:DSudar at lbl.gov <mailto:DSudar at lbl.gov>
>>> http://biosciences.lbl.gov/profiles/damir-sudar-2/
>>>
>>> Visiting Scientist, Oregon Health & Science University
>>>
>>>
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk
>>> <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>> --
>> 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
>>
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> <mailto:ome-devel at lists.openmicroscopy.org.uk>
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
> --
> Damir Sudar - Affiliate Scientist
> Lawrence Berkeley Natl Laboratory / MBIB
> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
> T:510/486-5346 <tel:510%2F486-5346> - F:510/486-5586 <tel:510%2F486-5586> - E:DSudar at lbl.gov <mailto:DSudar at lbl.gov>
> http://biosciences.lbl.gov/profiles/damir-sudar-2/
>
> Visiting Scientist, Oregon Health & Science University
>
>
> The University of Dundee is a registered Scottish Charity, No:
> SC015096
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> <mailto:ome-devel at lists.openmicroscopy.org.uk>
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
--
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
http://biosciences.lbl.gov/profiles/damir-sudar-2/
Visiting Scientist, Oregon Health & Science University
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