[ome-devel] OME developer doc

[Chris Armstrong]

Thank you Mark, this is very helpful. No doubt I'll be in touch with more questions :-)

Cheers,
Chris.

-----Original Message-----
From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Mark Carroll
Sent: 02 November 2015 10:19
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
Subject: Re: [ome-devel] OME developer doc

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

The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________
ome-devel mailing list
ome-devel at lists.openmicroscopy.org.uk
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

________________________________________________________________________
This e-mail has been scanned for all viruses by Star.
________________________________________________________________________