[ome-users] user feedback feedback

[Alastair Kerr]

We have been looking at the web and schoola interfaces for OME 2.4.0 and
have the following questions. We fully understand that this is very much
work in progress and we hope that the points raised are of some use to
the developers. 


In General:


The concept of the data hierarchy “Projects / datasets /
images/features” is not entirely compatible with our current structure
of archiving which tends to be “Date (year)/ Projects/ experiments /
data sets (including independent replicated data sets by date)/ images /
processed images / attributes (features)”. What is the best way to
relate the imposed hierarchy to real data acquisition – can a custom
hierarchy be defined? (this may be somewhat related to the Classifier
functionality but we are not clear how exactly to implement it?) 


Is OME able to import an existing directory structure (e.g. from an
archived DVD) and use this to automatically define projects / datasets,
perhaps through an interactive dialogue? Moreover can you allow
importing of images from nested directories by selecting only the top
level directory during image import (we tried it but failed to get
correct import). 


Related to the above – we remember that utilising an existing directory
structure was something that the “Catalyser” software could do quite
well. Is the Catalyser software still under consideration as a front end
for OME in this regard?


Currently it is unclear that while the Web interface is referred to as
“light” it seems to have more functionality than the Java interface?
Also we are not clear on the logic of the division of functionality
between the Java and web client – ultimately will all tasks (such as
image import, chain construction and execution of chains) be available
from the Schoola interface? 


Will any “wizards” be available as a pull down on the main menu bar when
you first open the program to step new users through common tasks? E.g.
defining of a project and data set followed by import of data;
extracting / modifying and adding image metadata; locating and viewing a
data set. This is perhaps the largest barrier to new users starting
using OME as the options and way to proceed are not always intuitive. 


Is there a list of data formats that can be read by OME as well as the
list of programs that can import OME XML format? At the moment we can
only ascertain whether a file format is compatible by reading the import
process notes. (For example are we correct in assuming that .avi moves
and Perkin Elmer Ultraview format are not supported).


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Java Client [using stable relase 2.4.0]:


Currently the “help” offers no content. It might be useful to replace
this with a hyperlink to the online “Getting started tutorial” resource,
that we find quite helpful, as a stop-gap to any planned expansion of
this functionality. 


Particularly in the case of the Java client, both the functionality
available and how to progress through operations is not intuitive. This
is complicated by the distribution of functionality between the Java and
Web interfaces.

Would it be possible to provide a working chains demo? I.e. downloadable
datasets coupled to a library of basic chains with which they will work,
to get people started? The current chain examples are not entirely clear
to us and possibly won’t even work with the data sets we are using.

There is clearly a great deal of functionality, however, much seems to
be “hidden” under “cryptic” icons or names, or requires the user to make
selection by direct or right mouse (ctrl+Mouse) in places other than the
intuitive locations and also having to confirm a requested action in
some cases by clicking another “button”. In this last case perhaps a
popup dialogue box asking to “continue or add/do another” might lead
users on better. By random clicking and reference to the helpful online
“Getting started tutorial” we could muddle through eventually, but his
does not seem like it would be appealing to primary Users (Post Docs and
PhD’s. 

It would be good to have more (all relevant?) functions duplicated in
categorised pull down menus on the relevant windows – if I can’t find a
function easily I find it useful to just browse the contents of pull
down menus to give me a hint what is available rather than browsing the
individual icon buttons.

Separate “editing”, “viewing” and “processing” workflows are defined but
I still find I keep accidentally skipping between them. Could they be
even better defined and separated out? This might be sorted out by
Wizards to get you used to the separate paths or by grouping the related
functionalities (editing/ viewing/ processing) under appropriately
labelled pull down menus.

Could the viewing of multi wavelength data be available in the image
view directly as well as under rendering?

Chains and chain builder do not fully convey to me what is intended. The
way of putting chains together is fairly intuitive however the amount of
info that pops up immediately is overwhelming to a novice user. The
navigator function (overview, a good idea) seems to be only
intermittently operational in our hands which causes confusion. It looks
like you should be able to draw a rectangle (red area) round the window
area you want to see from the overview but this does not always work. It
might be better if it could be expanded to a size where the text is
readable – or the full text replaced by a “title” for that section.
“Mouse-over” to highlight areas and the way mouse clicking in different
locations to expand and more contents within a window appears clumsy –
could simply clicking the section you want and having a fit to a window
which you could drag to size/shape not work better?

The ROI tool does not seem to allow local manipulation / analysis on the
part of the image defined by the ROI – would be good to be able to
resave the subregion or limit processing to that region. Tried to define
a subregion of an image stack to do subsequent processing to reduce the
processing time. Also tried to view local region to play as a movie – to
speed up the player (in our hands the possible play speed appeared to be
severely limited by the size of image, certainly well below the selected
play speed).


RMP/ARWK – 17/5/5