[ome-users] user feedback part II

[Alastair Kerr]

More Questions about OME use

23/6/5

We eventually got round to adding one of our previous queries into
bugzilla as requested (sorry for the wait, a confusion of responsibility
at this end). Here are some more user feedback. I hope this is useful to
you all.  
- Alastair 


Specific questions about use (OME 2.4.0)

Find Spots
we failed in our attempts to run the “find spots” analysis (Web UI) –
any ideas?
Error Message 
'There was an error executing this chain: Can't method
"attribute_sort_time" on an undefined value at
/usr/lib/perl5/site_perl/5.8.3/OME/Analysis/Engine.pm line 852'Note 

Note that the user had difficulty understanding the functionality. 
Perhaps this could be solved by additional documentation?


ROI
(update on previous question about ROI) Using the ROI definition tool
(shoola) – first open a single channel data set then set up an ROI and
apply. Slightly odd in the way it works: don’t get ROI analysis data
(analysis context) to work until you first go into “rendering” and
select greymodel (does not select this as the default) when tried on
MAC. With PC seems to recognise a channel and enter it but not do
anything until you click over the select channels and select Roi’s so
that they are both highlighted blue.


Import/Export of OME XML problems. 
An image file was exported from OME as OME XML format and then import
was attempted with the same filename. No error message but imported 0
images from 0 files.  Similar with a filename not already present in OME
but the OME XML file format generated by Imaris. Imaris did not import
an OME XML file outputted from OME but would reimport an OME XML file
that it generated itself from a Deltavision file format.
Error message from Imaris 4: “ (file type not recognised) “


ImageJ (setup with OME plugin with assistance from Curtis Rueden) had no
problem directly importing from OME, modifying the pixel data and
exporting back to OME as another pixel set under the same filename. What
should happen if you upload a file originally exported from OME to the
same dataset and image name? We were looking at this as a way to add
additional pixel sets to an existing data file. We have also struggled
with “create a custom annotation” “pixels” but it did not seem to add
the selected file data as a Pixel Set.



InstrumentsAnnotation
- When an instrument semantic type has been defined we still are unable
to return any hits when we search for “instrument’ but we can find hits
under ImageInstrument where we have linked image files to a defined
instrument as a custom annotation. If you then search again under
Imageinstrument it fails because it leave @Instrument in the “type” box.
Perhaps it is because we are currently putting in the instruments and
want to check which ones have been done, but it seems odd that you
cannot find instruments entered into OME unless they have been linked to
an image file. (is this true?)




General Questions about use:
- We are still having problems with Safari on the MAC and explorer on
PC. On the same machines FireFox works without problems.  We can get to
the login window but do not progress. We tried fiddling with setting for
cookies and popups without success. (I went though the list that Ilya
gave me last time. Given that firefox does work, the problem must be
client side. Damned if I can find a solution).
 
- Would it be fair to say that the best use of OME is (at least
currently?) with newly generated data inputted immediately after
collection, rather that for retrospective archiving of stored data from
CD’s / DVD’s – especially where the raw data has been processed to
generate further pixel sets?

- We have been looking to see if there is a function that lets you
specify that an image data set should be entered as an additional pixel
set on an existing image entry – a specific interest is where you have
raw and deconvolved image data sets as separate files to enter into OME
and combine under a single image file name. So far we have not been able
to accomplish this except through ImageJ.  Advice in achieving this
would be welcome. 

- we would really like some batch functions which would semi automate
the data upload process would be great even extending this to
annotations e.g. :
*import all files from a particular folder into OME under their
corresponding filenames – ideally with a dataset name taken by default 
from the folder (with the option to specify a different name).
* batch append annotations or other metadata to image sets (again
possibly as part of the import?) e.g. specify that all images came from
a particular instrument / objective / 
EX and EM wavelengths / require a particular OTF…

- Can chain builder be used to automate import in a batchwise way?

Related to the above, has anyone (Jason?) set up deconvolution queuing
that is able to collect batches of image data from OME, pass the
appropriate file format to the deconvolution algorithm and (after visual
inspection by the user) return the deconvolved pixel sets appended with
the deconvolution parameters?  Automation related to deconvolution would
be a key criteria for our routine use of OME. I might be able to write
some perl wrapper for this but some sort of perl API or code that I
could hack would be a big help. 


- We have looked at ways of organising data at the time of capture to
facilitate uptake by OME. Embracing the ideas of simple project/dataset
organisation and that a dataset should contain data of a similar type we
have tried file structures where the directories correspond to what will
be / are projects and datasets. Nested directory structures help
organise multiple treatments (condition variations) + controls +
dependent and independent repeat data and experiments, however, they
make upload into OME laborious.  A simple organisation of “folder = 
datasets” seems easiest if you name the files and folders well. 
 Using imaginative file naming always seems to break down eventually.
Any thoughts on naming / incrementing datasets and files would be
welcome. We have:
“user initials_date_celltype identifier_treatment identifier_repeat”.
Should OME automatically append incremental numbering/ identifying
lettering to datasets (like softWoRx DV file format appends filenames
according to incremental image number or processing steps)?

- It looks like raw data needs to be put onto OME as soon as possible
after collection, before any processing. Are there any projects
collaberating with softwre such as metamorph to include data import at
time of data capture?

We need assistance to find the way to add in missing specific metadata:
such as
Missing EX/EM data, and the objective used or which OTF to use/was used.
(We have started to store OTF images in OME) .
We found in shoola that you could view a table of image info data but
could not edit it (right click on preview image). With the image
displayed and from the Rendering / Channel Editor / Grey Model
information button there was an information table that could be edited
but not all of the input was remembered (only the excitation and dye).
On the image information no emission was specified, however the channel
was specified as emission 565. (Original data imported into a DV format
but collected using a custom cube on non-DV instrument – header edited
for deconvolution).

- We don’t see a way of deleting images from OME but can see that this
is a possible source of difficulties with incorporation of files into
multiple datasets potentially owned by different people. How do you go
about, firstly, dissociating an image from a dataset and deleting it
from  OMESIS? 

- In the Web UI the view of search has folder icons that don’t do
anything – could they be clickable to give a tree structure of the
project/datasets in a similar way to the Data Manager View or Hierarchy
browser in the Java Client. This would be especially useful if nested
datasets are included. (From a user who like programs such as file
explorer in windows). 













-- 
Alastair Kerr, Ph.D., 
Bioinformatician, Wellcome Trust Centre for Cell Biology,
COIL, Swann Building, The University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel: 44-(0)131-650-7527