[ome-users] OMERO COMMENTS AND PROBLEMS

[Jason Swedlow]

Hi Nicholas-

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.

Cheers,

Jason

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  
> community.
>
>
>
> In addition I have had a few problems (see below) for which I would  
> appreciate some help.
>
>
>
> Comments:
>
> 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?
>
> Problems:
>
>  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
>
> -------------------------------------
>
> Nicholas Vecchietti
>
> Istituto Cantonale di Microbiologia
>
> Via Mirasole 22A
>
> CH-6500 Bellinzona, Canton Ticino
>
> (Switzerland)
>
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