[ome-devel] OME developer doc

[Mark Carroll]

Dear Chris,

 > I am working on a project to develop some functionality for microscopy
> analysis, and one of the platforms of interest to us is OME. Please
> could someone point me in the direction of any developers’ documentation
> for OME?

There is actually quite a range to choose from.

For Bio-Formats, which is most useful for reading pixel data and
metadata from a wide range of image file formats, there is developer
documentation at
https://www.openmicroscopy.org/site/support/bio-formats/developers/ --
this used to focus on Java, along with the JACE-based C++ bindings to
that Java code, but we have recently expanded this documentation to
describe the current state of the work on our native C++ port of
Bio-Formats which already allows, for instance, writing OME-TIFF.

OMERO, which is the client-server system for managing the images, has
developer documentation at
http://www.openmicroscopy.org/site/support/omero/developers/

Those links are a recommended starting point for finding much of our
other useful documentation.

People often write client software to access their data on the OMERO
server via code in Java, Python, C++ or MATLAB. Especially for Java and
Python we offer extensive gateways filled with convenience functions for
helping you to accessing the OMERO server from client-side code, and you
can also work directly with the server API from the supported languages.
Both the API and gateways are quite well documented and you can read
about them in the main OMERO developer pages. For all these supported
languages, we offer a variety of training examples at
https://github.com/openmicroscopy/openmicroscopy/tree/develop/examples
but much of the other client-side code in the repository, ranging from
OMERO's Python-based command-line interface, to the Java and Python
integration tests, can also be drawn on as additional examples:
sometimes they include something very close to what one actually wants
to do oneself. For Python it's also worth seeing others' work in the
scripts repository at https://www.openmicroscopy.org/site/community/scripts

Both Bio-Formats and OMERO, even the OMERO server itself, include plenty
of classes that are intended for third parties to extend; indeed, many
have actually done so. These extension points range from authentication
to file transfer to new image file formats to extra information displays
in the graphical clients. Even for these cases there are often useful
examples and documentation: while most users never need to, it's often
possible to extend our actual codebase where necessary, and of course we
accept code contributions via pull requests.

Do feel free to browse around our website and our code repositories. If
you are looking to do something in particular, let us know more and we
may at least be able to bring to your attention the most relevant
documentation. Also, for specific problems in coding against OMERO or
Bio-Formats, this list is a great place to ask: we try to make it easy,
but OMERO is necessarily a complex system and we are always working on
ways to help others to use our software in the way that fits them best.

Cheers,

Mark

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