[ome-devel] CellProfiler on the cluster crashes OMERO

[Chris Allan]

Hello, Fredrick:

Comments inline.

On Thu, Dec 15, 2016 at 10:14 AM, Frederik Grüll
<frederik.gruell at unibas.ch> wrote:
> Hello Chris,
>
> Is there maybe a workaround, for example by loading the images not through
> OMERO but from the cluster file system? When I import a plate I select a HTD
> file and OMERO.insight uploads all the TIFFs of the plate along with it,
> with one TIFF per channel, and displays them as a multi-channel view as
> expected. I have four channels and would be interested in the filesystem
> location of the four TIFF files that back each image, and the information
> which TIFF belongs to which channel. I could then use this information to
> generate a CSV file for CellProfiler with paths instead of OMERO URLs.

You certainly could. However, as Jean-Marie has mentioned it's
potentially fairly involved and depends heavily on the Bio-Formats
reader implementation for the file format in question.

One additional option would be to utilise the "target" of Bio-Formats
along with the "series" available from the Image object to reconstruct
the Bio-Formats state on each CellProfiler initialisation.
Unfortunately I don't think CellProfiler can currently be instructed
to work with Bio-Formats in this way at the moment.

We've also made our pure Python OmeroReader implementation available now:

    https://github.com/CellProfiler/CellProfiler/issues/1772#issuecomment-268227790

>
> I had experimented a bit with image.getFileset() to get the original TIFFs.
> However, when I call the method, it takes a long time and then returns the
> paths of _all_ 9600 images of the plate, not only the paths of the four
> TIFFs I wanted. Is there a way to just get the paths to the TIFFs of a view
> only, plus the information which TIFF backs which channel?
>
> Cheers,
>
> Frederik

Thanks,

-Chris