[ome-users] OMERO COMMENTS AND PROBLEMS

[Nicholas Vecchietti]

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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