[ome-users] OMERO beta4 END USER impressions

Mon Apr 6 10:51:15 BST 2009

Dear OMERO developers and users,

as you know from the frequent postings from Mario Valle to this list,  
our OMERO / viral particle tracking project is moving along slowly  
but surely here in Southern Switzerland.

While Mario has been busy on the development side, I have spent some  
time test driving OMERO beta 4 from the END USER/scientist point of  
view.

First of all

CONGRATULATIONS on a GREAT RELEASE to all the DEVELOPERS!!!

This is really a quantum leap in the right direction and my feeling  
is that it will literally take off at the bench side in the next few  
months.
This is "the dawn of the age of OMERO"!

A part from all of these congratulatory notes, on the more useful  
side I would like to share a few comments I gathered after a very  
cursory first test drive of OMERO beta4.

Hope it will be useful

Best to all

Caterina

____________________
OMERO.webadmin

It offers basically the same functionalities of beta3 but with some  
great new features:

1. The HELP feature works well and is very useful
2. The GROUP AMIN feature is very nice and useful, helping the  
ADMINISTRATOR to administer GROUP assignments of individual SCIENTISTS.

OMERO.clients

(.importer, .insight and .editor)
OMERO.importer

Test of import capabilities:

.tiff, .stk, .lsm, .liff imported correctly in the DB

.lif failed

(The error message was reported through the DEBUG message board and  
also to the OME user’s listserve in a separate post).

Importing into newly created PROJECTs and DATASETs

I noticed a problem during import when a new PROJECT is created by  
the add command in the Import Settings tab of the Import Window.

When a new PROJECT is added to the DB by the OMERO.importer, it is  
not visible in the hierarchical tree structure of DATA NAVIGATION  
panel of the OMERO.insight work space. The PROJECT is created but it  
is not visible in the tree.

On the other hand, when a new DATASET is added as part of a new  
PROJECT by the OMERO.importer, it is visible in the OMERO.insight  
DATA NAVIGATION panel but it appears listed at the incorrect tree  
depth (listed at the PROJECT depth instead than the level of  
DATASET). This problem does not manifest itself when a new DATASET is  
added as part of an existing PROJECT.

OMERO.insight

General comments

  First off, CONGRATUALTIONS on a JOB well done!

The general comment is rally extremely positive.
Starting from extended METADATA handling capabilities (see below on  
specific problems), to the new DYNAMIC WORKING AREA (I love being  
able to move images around on the workspace, this feature is really  
great to be able to sort through, classify and organize data  
following different and parallel criteria), the SEARCH feature, the  
interfacing with OMERO.editor and the HELP availability... the leap  
forwards is really clear and palpable.  This is really the way forwards!

Specific comments and bug-reporting
METADATA HANDLING:

Metadata divided in GENERAL and ACQUISITION is very nice and useful  
because it allows different levels of involvement on the side of the  
user.
Metadata GENERAL: I like the clear and unequivocal sub-division  
between the COMMENTS, ATTACHMENTS and EXPERIMENTAL PROTOCOL metadata  
and the more technical information about the IMAGE data.
Metadata ACQUISITION: in general this looks great (but see some  
specific problems listed below).
GENERAL PROBLEMS
There still is an issue with being able to edit un-set or wrongly  
filled fields. It is not clear if more editability by user will be  
provided later… For now it is not available and critical METADATA  
information cannot be recorded. This is critical for usability.

Specific examples of problem areas (this is not a complete list, it  
is provided to give an example of the kind of problems I am talking  
about):
ACQUISITION.IMAGE.ENVIRONMENT these fields have to be able to be set  
by user as they are rarely stored in data files
ACQUISITION.CHANNEL.CAMERA fields, same as above, it is useful to  
store but has to be filled in in many cases

INDIVIDUAL IMAGE FORMAT PROBLEMS
.stk (Metamorph)
GENERAL fields were OK except for the "Pixel Size" field
ACQUISITION fields not populated

.lif (Leica)
IMPORT FAILED (see also above)

.lsm (Zeiss)
GENERAL fields were populated correctly
ACQUISITION only partially populated. Was able to differentiate  
correctly between a CONFOCAL channel and a transmission light channel.
.tiff (various sources)
GENERAL fields were populated correctly
ACQUISITION minimally populated, probably reflected correctly the  
data recorded on the file format
·      .liff (OpenLab)

GENERAL fields were populated correctly
ACQUISITION minimal and sporadic, may reflect the original file format

DATA ORGANIZATION

Deleting data from DB
·      Full deletion capabilities works nice at all tree-structure  
levels. This is really nice.

Data organization
·      Moving between PROJECTS and DATASETS this is a working really  
great

·      Dynamic data display on Working Area is a very nice new  
feature. The ability of organizing the images on the virtual  
workspace, will be very useful to be able to organize, classify and  
tag images as appropriate.

RENDERING engine

General comments
This feature is great but still too slow for full usability.
ROI tool is still below standard.
This has to be clearly high on the PRIORITIES list now that beta4 is  
out.

Specific problems
1.     I still was not able to find the facility for being able to  
batch-apply same RENDERING SETTINGS to entire DATASET or PROJECT.

Being able to apply rendering settings across images is essential for  
usability.

Especially CRITICAL if import fails to map the rendering colors the  
biologist is most used to (Green for GFP, Red for RFP etc.).

2.     Had a specific problem (BUG) when trying to copy and paste  
RENDERING SETTINGS from one image to another.

While working on a DATASET of  .lsm images the application gave an  
error after I copied the rendering settings and tried to paste to a  
new image. The error was:  "No Image's settings to paste". This must  
be a bug.

SEARCHING

This feature works very nicely as far as the limited test I have done.
Being able to fully search using attached files, OMERO.editor  
generated protocols, web attachments on top of comments and tags  
(already possible) will be critical for full usability.

Specific comments
On a positive note, a very nice feature was the ability of creating  
new DATASETS containing the results of the search.

On a negative note, Was not able to keep track of the search results  
when getting back to the DATA VIEWER mode.  It would be useful to for  
example highlight or somehow keep track the results once back in the  
DATA VIEWER in order to be able to work on the images found in the  
context of the remaining images. This is rendered even more difficult  
by the fact that in the "View as a Table" tab one does not see what  
PROJECT or DATASET the images belong to. The information is stored in  
right most panel but this is a little clumsy.

EXPORTING

Nice EXPORT feature works well and is very useful for SHARING and  
PUBLISHING data

OMERO.editor

This new client has the potential for being very useful and it very  
well conceived. I love the ability of being able to create new  
protocols and also fill in parameters values when creating an  
EXPERIMENT from a certain protocol template. More specific comments  
to follow

____________________________
Caterina Strambio De Castillia, Dottore in Biologia, PhD

Biologiste 2 - Senior Research Scientist
Laboratory of Viral replication, pathogenesis, and immunity
http://www.mimo.unige.ch/luban_lab/

Department of Microbiology and Molecular Medicine
University of Geneva
1 Rue Michel Servet
CH-1211 Geneva 4
Switzerland

Phone: +41-22-379-5720
Fax: +41-22-379-5702

****
Visiting Fellow
Laboratory of Cellular and Structural Biology
http://www.rockefeller.edu/labheads/rout/research_project_3.php

The Rockefeller University
1230 York Avenue
New York NY 10065
______________________________
Caterina Strambio De Castillia
via Monte Crenone 1
6500 Bellinzona
Svizzera

+41 91 8252701
+41 78 7367537

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