[ome-users] What did OME ever do for us?

Mon Jul 18 14:52:40 BST 2005

Hi Graham-

On 18 Jul 2005, at 08:21, Graham Klyne wrote:

> (with apologies to Monty Python and others for the subject line...)

;-)!

>
> Now that I have OME up and running and able to import microscope  
> images, I am exploring the extent to which it can help us with our  
> image+annotation requirements.  I have some specific questions, but  
> first I'll try and outline what we're trying to do, in case we're  
> trying to do something that isn't reasonable to expect OME to handle.
>
> ...
>
> The research project I'm supporting aims to create a database of  
> images of in situ gene expression in drosophila testes.  To create  
> these images, the researchers go through a fairly involved process  
> of gene selection, gene expression analysis and in situ gene  
> expression image creation. Image acquisition is very much toward  
> the end of the overall experimental procedure, and the resulting  
> images are not (in the current procedure) subjected to subsequent  
> computer analysis.  What we do want to do is to cross-refer the  
> images to details of genetic and other information from preparatory  
> steps, and also to capture researcher annotations at the time of  
> image acquisition (noting that researchers can often see more  
> through the microscope than they can see in the resulting computer  
> images).

Understood-- these are all critical features for many users including  
our own.

>
> At the present time, we're not trying to use OME for capturing the  
> preparatory information.  What I am trying to do is use OME to  
> capture researchers' observations and annotations in a structured  
> form at the point of image acquisition and importation to OME, with  
> the possibility of adding additional annotations later.  These will  
> later be combined with the genetic information and researchers  
> conclusions to create a database for final publication.
>
> From this, I hope it's clear that what is important to us is  
> capturing researchers' observations and annotations about images,  
> rather than automated image analysis, which appears to be OME's  
> primary target.  The incorporation of annotation as an OME "module  
> execution" seems to support this kind of use, but I'm not sure how  
> the annotation features are intended to be used.

Some very important things to understand:

-- OME is not a "completed" project; the kinds of requirements you  
have are similar to our own (my lab at Dundee).  Working through all  
the requirements for sophisticated annotation, providing enough  
structure (but not too much), is exactly where we are trying to go.   
In our current vision, this is a part of what we term "data  
management" as opposed to data analysis.  The two are by no means  
mutually exclusive.

-- There are multiple parts to  the OME project.  The two germane to  
your questions are 
1) the backend and API, which we have set up to store as much about  
an imaging experiment as possible-- it holds lots of the OME concepts  
you are familiar with;
2) the UIs, that allow a user to actually access OME's functionality.

To be frank, we worked hard on the backend for many years, only to  
have a backend, and not much more-- we always had a web UI, with some  
very importnat functionality, but real limitations given what a web  
browser can and can't do.  Our UIs have been developing for the last  
18 months, and we are hoping to provide more functionality, with  
better performance, over the next 6 months.  Our two UIs are  
complementary and non-overlapping, with good reason.  But do play  
with them-- there is lots in both, ut it may take some scratching  
beyond the surface.

>
> ...
>
> So to my specific questions:
>
> 1. How are custom annotations intended to be used?
>
> 2. How to create new annotation metadata structures?
>
> Details follow.  If these questions are answered in existing  
> documentation, please just provide pointers.
>
>
> 1. How are custom annotations intended to be used?  I have tried to  
> use custom annotations as follows, using the web browser interface:
> - create a dataset and import an image into that dataset
> - I have successfully created "DatasetAnnotation" and  
> "DatasetTestSignature" annotations for the dataset by selecting the  
> corresponding listbox entries and clicking on "Create a custom  
> annotation".  (I don't know if the values I entered make sense, but  
> they have been stored and are retrievable as part of the dataset  
> metadata.)
> - I then tried to use a similar procedure to create a custom  
> annotation for the image.Selecting "ImageExperiment" as the type of  
> custom annotation, I am asked to create an "Experiment" and an  
> "Experimenter", which I duly do, filling in all the proffered  
> fields and clicking the corresponding "Create ..." buttons.
> - The "Image experiment" dialog ends up with an experiment  
> identified by a number ("38" in my case) and an image (the one I am  
> annotating), but nothing that seems to reflect the information just  
> entered.  Clicking on "Create image experiment" returns me to the  
> original screen, but it's not obvious that the annotation has been  
> added.  (I now notice that it appears in the "Module execution"  
> list, but not at the top or bottom of the list.  The first time I  
> tried something like this, the new information appears to have been  
> lost.)
>
> My question is:  the above procedures seem non-obvious and error  
> prone; are they consonant with how the annotation feature is  
> intended to be used, or am I overlooking something?

As I understand it, you have missed completely the CategoryGroup/ 
Category functions.  You will see these on the page where you view a  
specific dataset-- note the text ""To cluster thumbnails by  
category....".  We think of this as an alternative set of user- 
definable hierarchies.

This is a user defined CategoryGroup, including a set of Categories.   
A screenshot of my own customised annotations, for one of my  
Datasets, is attached.  The bottom line-- OME defines a group of user- 
defined phenotypes as Categories, and the grouping of these as a  
CategoryGroup.  An image can belong to only one Category **within** a  
CategoryGroup, but can belong to multiple Categories within different  
CategoryGroups.  Both the Java and web UI's support this functionality.

Note that you can use these annotations for the purpose you are  
thinking, but there isn't much structure to them-- yet.  They are  
really meant, currently at least, t suppport free text annotation,  
which is a very different beast than the CategoryGroup/Category  
functions

>
>
> 2. How to create new annotation metadata structures?  A simpler  
> question with, I suspect, a more complex answer, but hopefully one  
> that can be addressed by a pointer to relevant documentation.
>
> We aim to capture data in a semi-structured form that can be  
> exported to a semantic web database for further cross-referencing  
> with other information sources.  The built-in custom annotations  
> seem to support the right kind of general structures for this  
> purpose.  Are the form displays linked directly to the XML metadata  
> schema, or is there an additional presentation-description  
> component?  How do I go about adding additional metadata to OME?   
> Can the metadata format be dynamically updated, or does this  
> require a re-build of the database?
>

Both the Java and web clients support this, using the CategoryGroup/ 
Category Functions  (see http://openmicroscopy.org/getting-started/ 
manual_classification.html  and http://openmicroscopy.org/getting- 
started/datasetbrowser.html).  The usage of OME for these purposes is  
not well documented, except for these pages.  it's coming, honest.....

One last point.  A  MAJOR (in my mind, at least...) limitation of  
this functionality is the limit that there are really on two levels--  
CategoryGroups and Categories.  We are still working on this,  
especially from the UI standpoint, but expect this to be fleshed out  
in later versions.

Hope this helps.

Cheers,

Jason

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