[ome-devel] Update on OMERO and HCS

Wed Oct 19 15:53:42 BST 2011

Hi Harri,

> here is a quick explanation to give a rough idea:
> 
> 1. Leica Matrix Screener:
> 
> The output is organized in folders like this:
> experiment--2011_04_20_07_15_22/slide--S00/chamber--U00--V00/field--X00--Y00/image--L0000--S00--U00--V00--J08--E00--O00--X00--Y00--T0000--Z00--C00.ome.tif
> 
> As you see, both the directory names and the file name tell about
> the well (chamber) and the field. The output files are OME tifs,
> with metadata about the microscope settings etc. The output file
> name indicates the channel (C00), timepoint (T0000), z-position in
> stack (Z00), loop number (L00) etc.

We do already have plans to support this format:

http://trac.openmicroscopy.org.uk/ome/ticket/4154

> 2. Cellomics Cell Insight
> 
> The contents of the data folder look like this:
> MFGTMP_110331130007_H10f02d0.C01
> MFGTMP_110331130007_H10f02d1.C01
> MFGTMP_110331130007_H10f03d0.C01
> MFGTMP_110331130007_H10f03d1.C01
> MFGTMP_110331130007.MDB
> 
> Again you can the filenames indicate well (H10) and field (f02, f03)
> and channel (d1, d0).
> 
> There is also a MS Access database file with info, which can be
> accessed with mdbtools.

Bio-Formats can currently read .c01 files, and will attempt to parse the
well and field information from the file names.  However, metadata from
the associated MS Access database is not parsed, as we do not have any
examples of this database file.

I would recommend that you try importing your .c01 files first, and see how
well it works - we have a limited number of test datasets, so it maybe
that some improvements are necessary to correctly import your datasets.

> What is your first impression, would it be difficult to create a
> reader? I think just getting the data in OMERO would be a big step
> for us, because then we could really see how the whole setup works,
> performance, integration with the rest of the system. Then if it
> looks like the way to go, we could go ahead and think about the
> difficult part with analysis results.

I don't think it will be particularly difficult to get your data into
OMERO, provided that you can send at least one Leica Matrix dataset and
at least one Cellomics dataset that includes the .mdb file.  I will send
you a private email with information on how to send files to the OME
developers.

Regards,
-Melissa

On Wed, Oct 19, 2011 at 03:49:18PM +0300, Harri Jäälinoja wrote:
> 
> Hi Jason,
> 
> here is a quick explanation to give a rough idea:
> 
> 1. Leica Matrix Screener:
> 
> The output is organized in folders like this:
> experiment--2011_04_20_07_15_22/slide--S00/chamber--U00--V00/field--X00--Y00/image--L0000--S00--U00--V00--J08--E00--O00--X00--Y00--T0000--Z00--C00.ome.tif
> 
> As you see, both the directory names and the file name tell about
> the well (chamber) and the field. The output files are OME tifs,
> with metadata about the microscope settings etc. The output file
> name indicates the channel (C00), timepoint (T0000), z-position in
> stack (Z00), loop number (L00) etc.
> 
> 
> 2. Cellomics Cell Insight
> 
> The contents of the data folder look like this:
> MFGTMP_110331130007_H10f02d0.C01
> MFGTMP_110331130007_H10f02d1.C01
> MFGTMP_110331130007_H10f03d0.C01
> MFGTMP_110331130007_H10f03d1.C01
> MFGTMP_110331130007.MDB
> 
> Again you can the filenames indicate well (H10) and field (f02, f03)
> and channel (d1, d0).
> 
> There is also a MS Access database file with info, which can be
> accessed with mdbtools.
> 
> 
> What is your first impression, would it be difficult to create a
> reader? I think just getting the data in OMERO would be a big step
> for us, because then we could really see how the whole setup works,
> performance, integration with the rest of the system. Then if it
> looks like the way to go, we could go ahead and think about the
> difficult part with analysis results.
> 
> Best regards,
> Harri
> 
> On 09/10/11 23:45, Jason Swedlow wrote:
> >Hi Harri-
> >
> >On 7 Oct 2011, at 13:16, Harri Jäälinoja wrote:
> >
> >>
> >>Dear Jason,
> >>
> >>this looks very interesting. Would it be possible to display also
> >>image analysis results attached to the original images? It would be
> >>great to have an easy access to segmentation and/or object recognition
> >>results, to have the possibility to check how the analysis has worked.
> >>
> >
> >We definitely can display ROIs-- identified objects, etc., and these can
> >be linked to features calculated from these images. One of the
> >challenges here is that these are usually fairly custom (even from
> >commercial platforms, there are often many different ways of calculating
> >and storing results). We have achieved this for specific situations.
> >
> >
> >>Actually I have never seen how the HCS support in OMERO is currently,
> >>because OMERO doesn't have readers for our HCS systems. In our unit we
> >>have a Cellomics CellInsight and a Leica HCS-A. How is the situation,
> >>are there any plans to add support for these?
> >
> >As always, our support for file formats, via Bio-Formats, depends on
> >great sample data sets. If you have these, we can definitely add it to
> >the Bio-Formats to-do list.
> >
> >>Both image formats are supported, so that's not a problem. Just the
> >>plate level reading is missing. I will have look at the code for the
> >>existing HCS readers, but I don't know if I have enough time or skills
> >>to implement something.
> >
> >If you mean plate metadata (wells, detectors, channels, etc), that
> >should be straightforward. If you mean analysis results from calculated
> >features, that is certainly more work, and often quite custom. Let us
> >look at the data, and we can tell you what's possible.
> >
> >Cheers,
> >
> >Jason
> >
> >>
> >>Best regards,
> >>Harri
> >>
> >>
> >>On 02/10/11 10:57, Jason Swedlow wrote:
> >>>Dear All-
> >>>
> >>>Just an update on our activities with OMERO and HCS data.
> >>>
> >>>At the beginning of September, the Journal of Cell Biology published
> >>>four HCS screens on the JCB DataViewer (a custom version of OMERO, built
> >>>and maintained by Glencoe Software), totalling about 300 GB of data. The
> >>>first was a genome wide screen of the S. cerevisiae non-essential
> >>>collection, looking for modifiers of the DNA repair pathway. This was
> >>>essentially a "re-publishing" of a previously published paper. The new
> >>>paper is at:
> >>>
> >>>http://jcb.rupress.org/content/194/5/665
> >>>
> >>>and the data is at:
> >>>
> >>>http://jcb-dataviewer.rupress.org/jcb/browse/4608/S1/
> >>>
> >>>Maybe most useful to click on the "Chart" button.
> >>>
> >>>A second paper, which looked for modifiers of actin structure in cells,
> >>>used one screen in Drosophila cells and two targetted screens in human
> >>>cells: The paper is at:
> >>>
> >>>http://jcb.rupress.org/content/194/5/789
> >>>
> >>>and the data is at:
> >>>
> >>>http://jcb-dataviewer.rupress.org/jcb/browse/4609/
> >>>
> >>>The presentation of the data there can be debated-- there are advantages
> >>>and disadvantages to what was done, and the decisions were made by many
> >>>people. For example, we think we can do a better job at visualising the
> >>>plates and their content. However, as a scientist, I do like the
> >>>browser-based view of the screen results, that shows what the authors
> >>>scored as hits, and allows me to browse their interpretation of the
> >>>results.
> >>>
> >>>Data download is enabled at the level of wells (and thus individual
> >>>genes) at the moment. Plate-based data download is coming.
> >>>
> >>>This custom UI was built by Glencoe Software, under contract to
> >>>Rockefeller University Press. As always, this code is being rolled into
> >>>the GPL-released version of OMERO. We have some versioning issues to
> >>>reconcile, but getting these facilities into the open source codebase is
> >>>a major priority. We'll send updates on this list as the code becomes
> >>>available.
> >>>
> >>>Let us know if you have any questions about this resource, the code or
> >>>our steps going forward.
> >>>
> >>>Cheers,
> >>>
> >>>Jason
> >>>
> >>>
> >>>
> >>>**************************
> >>>Wellcome Trust Centre for Gene Regulation & Expression
> >>>College of Life Sciences
> >>>MSI/WTB/JBC Complex
> >>>University of Dundee
> >>>Dow Street
> >>>Dundee DD1 5EH
> >>>United Kingdom
> >>>
> >>>phone (01382) 385819
> >>>Intl phone: 44 1382 385819
> >>>FAX (01382) 388072
> >>>email: jason at lifesci.dundee.ac.uk <mailto:jason at lifesci.dundee.ac.uk>
> >>><mailto:jason at lifesci.dundee.ac.uk>
> >>>
> >>>Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
> >>>Open Microscopy Environment: http://openmicroscopy.org
> >>>**************************
> >>>
> >>>The University of Dundee is a Scottish Registered 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
> >>
> >>
> >>--
> >>__________________________________________________
> >>Harri Jäälinoja
> >>Light Microscopy Unit
> >>Institute of Biotechnology, University of Helsinki
> >>http://www.biocenter.helsinki.fi/bi/lmu/
> >>+358 9 191 59370 fax +358 9 191 59366
> >>
> >>_______________________________________________
> >>ome-devel mailing list
> >>ome-devel at lists.openmicroscopy.org.uk
> >>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> >
> >
> >
> >**************************
> >Wellcome Trust Centre for Gene Regulation & Expression
> >College of Life Sciences
> >MSI/WTB/JBC Complex
> >University of Dundee
> >Dow Street
> >Dundee DD1 5EH
> >United Kingdom
> >
> >phone (01382) 385819
> >Intl phone: 44 1382 385819
> >FAX (01382) 388072
> >email: jason at lifesci.dundee.ac.uk <mailto:jason at lifesci.dundee.ac.uk>
> >
> >Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
> >Open Microscopy Environment: http://openmicroscopy.org
> >**************************
> >
> >The University of Dundee is a Scottish Registered Charity, No. SC015096.
> >
> >
> >
> 
> 
> -- 
> __________________________________________________
> Harri Jäälinoja
> Light Microscopy Unit
> Institute of Biotechnology, University of Helsinki
> http://www.biocenter.helsinki.fi/bi/lmu/
> +358 9 191 59370 fax +358 9 191 59366
> 
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