Import whole slide image with annotations

Hello, is there any way to import whole slide image ndpi with annotaitons ndpa into OMERO? Does it need any conversion?

Hi @olatarkowska,

at least from the Bio-Formats perspective, at the moment, the NDPIReader which handles the Hamamatsu NPDI format will only detects and reads .ndpi files i.e. the binary files containing the WSI.

If you wat to read the ndpa file in addition to the imaging data e.g for importing into OMERO, you would need some additional translational code that is aware of the file format, can parse the content of the file and optionally convert it into a compatible format.

We are not aware of a public specification or official representative samples of the ndpa file format. OpenSlide might be a good starting point as the Hamamatsu NDPI reader has some existing support for ndpa files. Others in the community might be able to report about alternative existing options.

We have just come across this same problem with a legacy set of annotated ndpi images. Does anyone know if anything has become available since the date of this original post in August?

No news from the @OMETeam, @PaulNSchofield. ~J.

@PaulNSchofield check it may help you as an example


…and this post from EP.Zindy earlier today: Importing NDPA annotation files into QuPath (code attached)

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