Bio-Formats: Support for OCT Devices

[schlto]

Hi everybody!

Me and a group of researchers are currently working with different Optical Coherence Tomography (OCT) formats for retinal imaging and analysis. Those formats include a wide range of mostly undocumented interfaces for manufacturers like Eyetec, Heidelberg, Nidek and Topcon.

The reason I'm writing you is because our project is entirely written in C++ and therefore most likely not compatible with the Java implementation of Bio-Formats. Could you make use those formats if we translated our project into Java, or is there an alternative way*?

For further informations just ask me or have a look at our repo and short wiki, https://bitbucket.org/uocte/uocte/wiki/Home.


Thank you for your time!
Tobias

[sbesson]

Hi Tobias

The reason I'm writing you is because our project is entirely written in C++ and therefore most likely not compatible with the Java implementation of Bio-Formats. Could you make use those formats if we translated our project into Java, or is there an alternative way*?

We had a couple of questions/request about the support of OCT formats like the Heidelberg file format. In the general sense, we are always interested by the community expertise for new file formats and modalities. It would be really good to discuss how to make efforts converge and integrate contributions.

On the technical front, it would be interesting clarifying what translating into Java would mean. From our experience, there are two options to add such support:

• either by completely converting the code as a new Java-based format reader
• or by writing a Java reader wrapping a C++ library. This strategy is used by the native 3i Slidebook reader

For further informations just ask me or have a look at our repo and short wiki, https://bitbucket.org/uocte/uocte/wiki/Home.

Thanks for making this information publicly available and we should definitely keep the back and forth using public threads like this one.

Best,
Sebastien