[ome-users] OMERO COMMENTS AND PROBLEMS
jason at lifesci.dundee.ac.uk
Sat Apr 2 00:39:54 BST 2011
Thanks so much for this feedback-- hugely helpful. Jean-Marie and
others will be in touch with some specifics-- some of these we already
have targeted, others are very useful to have.
Please keep all suggestions and critiques coming-- that's what makes
the software better!
As always, thanks for your support.
On 31 Mar 2011, at 19:44, Nicholas Vecchietti wrote:
> Hi everybody,
> I have been working with Caterina on my master project at the
> Microbiology Institute of Canton Ticino in Southern Switzerland and
> I am using OMERO quite actively.
> Using OMERO has been truly a life saver for my project allowing me
> to manage large numbers of images, keeping track of several
> experiments I am conducting in parallel and classifying images based
> on quality and content.
> After several months of usage I have gathered a couple of comments
> about OMERO which I thought might be useful to share with the
> In addition I have had a few problems (see below) for which I would
> appreciate some help.
> 1) In the last version of the OMERO clients (v4.2.1) I notice that
> the "slide show" feature was eliminated. Is there a reason why? It
> was very useful for rapidly comparing several images. Are you
> considering re-introducing this or some other tools for the purpose
> of comparing several images
> 2) I think it might be useful overall to add a new hierarchical
> level for image management which would sit below the DATA SET level
> allowing more flexibility in classification of image data.
> 3) I have noticed that "comments" cannot be modified once assigned
> to individual images.
> I think that it would be quite useful to consider allowing users to
> erase comments they have made to images as this would enable a more
> dynamic use of this feature.
> Would this be possible?
> 4) OMERO.insight tends to freeze after 15-20 minutes of active use.
> The problem gets solved by relaunching the client but this is
> obviously not ideal for a busy OMERO session.
> Any idea of why this is happening and how to solve it?
> 5) When I load single channel 8-bit tiff images acquired using the
> AxioVision v 4.6 driven AxioCam MRc Camera, they get imported into
> OMERO as three-channels images with the 3 RGB colors channels.
> This is a problem as it creates an undue processing burden.
> Any idea as to why this might be happening?
> In case it might help to trouble shoot the problem I can send an
> example image. Also, I have noticed that FIJI (which also uses
> BioFormats) reads the same files correctly and displays them as
> single 8bit images.
> 6) When working with .lif files from Leica, I have encountered
> problems with the assignment of the correct label to each individual
> color channels.
> As an example recently I have had to import .lif files containing
> multiple single plane images each acquired with two channels which
> in the Leica software I had named Leica/DAPI and LEICA/Cy3.
> Upon import OMERO appeared to handle these names quite
> inconsistently, a minority of the times the names were assigned
> correctly to each channel while the majority of instances both
> channels were assigned the name Leica/DAPI.
> This is obviously a problem as once imported the names are fixed and
> this will create considerable confusion down the line.
> Any idea of what is happening and how to solve it?
> Again I want to emphasize that despite these minor problems, OMERO
> has been really great to use and quite reliable.
> I hope these comments and question will contribute to make this
> software even more useful and widespread.
> Thanks for your attention
> Nicholas Vecchietti
> Istituto Cantonale di Microbiologia
> Via Mirasole 22A
> CH-6500 Bellinzona, Canton Ticino
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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