Open Microscopy Environment

Hi,
I am developing a software which is aimed to connect to external databases, search ( e.g. free format search on metadata related to images) and fetch data out of them. I developed my connection to PDB (Protein Data Banks) using their APIs. However, I could not find APIs for free format search or key-value search on OMERO.

Could you please help me how I can search on metadata related to images?

Best regards,
pz3977

I'll answer your question in the context of OMERO 5.0.3 which is due to be released within the next week, and contains several updates to the Lucene-based "free format" searching functionality in the clients and server.

The Python BlitzGateway searchObjects() has a few extra parameters:

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searchObjects(obj_types, text, created=None, fields=(), batchSize=1000, page=0, searchGroup=None, ownedBy=None, useAcquisitionDate=False):


This will return you a list of the specified objects where 'obj_types' is a list of

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["Project", "Dataset", "Image", "Screen", "Plate", "Well"]

E.g.

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>>> for i in conn.searchObjects(["Image"], "tiff"):
>>>     print i.getName()
>>>     
Fig 1A-1min.ome.tiff
Fig 1A-5min.ome.tiff
Fig 2A.ome.tiff
6x4y1z1t1c8b-swatch-2s2p4w2ws.ome-v2010-06.ome.tiff


I just created a script with examples of using all the other parameters
https://gist.github.com/will-moore/e5fe45145fbfc5494127


For key / value searching, you really need to query the Database directly, which requires some knowledge of the OME model.

Have a look at this "Metadata search" example https://gist.github.com/will-moore/5782 ... rch-py-L13

This is an OMERO script which adds Metadata search functionality to the OMERO clients if you add the script to the server, but should give you some ideas for how to query some fields of the DB.

Hope that helps,

Will.

Hi Will,

Thanks for the complete reply and my apology for late reply. I was not working last week.
I wondered if OMERO.py version 5.0.3 is available. I could not find a link for download!

Best regards,
Parisa

Hi Parisa,

sorry for the delay. We found a few last minutes bugs in the 5.0.3 release candidates and are hoping now to have a build this week. You can either build from the `origin/dev_5_0` yourself, or use one of the builds from http://ci.openmicroscopy.org/job/OMERO-5.0-latest/?. For example, if you have Ice 3.4 installed, you can look here:

http://ci.openmicroscopy.org/job/OMERO-5.0-latest/ICE=3.4,label=ome-c6100-1/lastSuccessfulBuild/artifact/src/target/

Cheers,
~Josh.

Hi Josh,

Thanks for the reply. Since I am very new to OMERO and python , I prefer to use a ready version with minimum number of bugs. I have Ice3.4 installed but I could not find Omero.py v 5.0.3 in

http://ci.openmicroscopy.org/job/OMERO- ... rc/target/

Should I build some thing? If your release is coming this week, I prefer to wait more few days and get a stable version.

Regards,
pz3977

pz3977 wrote:If your release is coming this week, I prefer to wait more few days and get a stable version.

That makes complete sense. The release will be announced here on the forums and on the mailing lists.
~J.

Hi,
First of all I want to thank you for improving search functionality in new version. I was looking forward to using it. Then I would like to ask the following questions:

1. Is there any way to search a keyword without specifing the field name? As it is mentioned in https://gist.github.com/will-moore/e5fe45145fbfc5494127, I could search a keyword which exists for example, in file.contents:

for i in conn.searchObjects(["Dataset", "Image"], "tiff", fields=["file.contents"]):
print i.OMERO_CLASS, i.getName()

In order to search a keyword which may exists in any field, is there any solution?(Does fields=[] works?)) or Can I search all metadata using following code?

for i in conn.searchObjects(["Dataset", "Image"], "tiff"):
print i.OMERO_CLASS, i.getName()

2. I was wondered about the regular expression which is used for search. In my experiment, it could not find the image, when part of text (the last part) in its metadata is being searched.

3. How can I search metadata releated microscope settings? Are the search fields limited to 'name', 'description', 'annotation', 'file.name', 'file.format', 'file.contents', 'file.path' or I could find other metadata as well?

Best regards,
pz3977

Hi,

Maybe you missed the first example at https://gist.github.com/will-moore/e5fe45145fbfc5494127 for searching without specifying fields (just as you'd guessed):

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for i in conn.searchObjects(["Image"], "tiff"):
   print i.OMERO_CLASS, i.getName()


To build the Lucene search index, we generate keywords from text by splitting on non-alphanumeric characters. So, to find eGFP-H2B you'd need to search for *GFP or eGFP or H2B or H2*, but not GFP. You can read a little more about this at the user-guide: http://help.openmicroscopy.org/search.html.

For metadata search, did you look at https://gist.github.com/will-moore/5782 ... rch-py-L13? You can upload this script directly to the OMERO server since it is an OMERO.script (as described here http://www.openmicroscopy.org/site/supp ... oad-script) and you will have a basic metadata search UI available in the clients under the scripts menu.
Or you can just use the code examples. It gets a little tricky since you have to have some knowledge of the OMERO model to build the correct DB query. But that should at least get you started.

Hi wmoore,

Many thanks for the reply. As you said, I tried to upload Metadata_Search.py which is provided in https://gist.github.com/will-moore/5782 ... rch-py-L13, to check how metadata search works, however, it does not identify "script" keyword. Following are the steps which I did:
Since I do not have any server locally installed, I tried to connect to server ""omero.ohsu.edu"" to upload the script:(using OMERO.py)
$ bin/omero shell --login
server..
login..
pass..
in[1]: omero script upload Metadata_Script.py --official

the error : invalid syntax, pointing to "script"

I appreciate it if you could help me. How can I upload and use the script without locally installed server?

Regards,
pz3977

You don't need to use the shell. Simply do this:

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$ bin/omero script upload path/to/Metadata_Script.py --official


and you will get asked for server and login details if you are not already logged in.
You'll need to be an admin to upload 'official' scripts.

Then look in the scripts in the clients and you'll see the script under whatever path/to/Metadata_Script.py you used above (so it helps to get this right if you want other users to find scripts in the 'right' place).

Hope that helps,

Will.