search

glencoesoftware / bioformats2raw

Bio-Formats image file format to raw format converter
GNU General Public License v2.0
77 stars 35 forks source link

Conversion directly from imageplus #110

Closed K-Meech closed 3 years ago

K-Meech commented 3 years ago

Is there any way to give bioformats2raw an imageplus, rather than the filepath to an image? For some use cases (e.g. converting image sequences of many individual tiff files or pngs), it would be very useful to be able to open in imageJ, and then convert to zarr from there.

Thanks for your help!

chris-allan commented 3 years ago

No, not really.

The goal of the project is to, in as performant a way as possible, take Bio-Formats reader input and produce Zarr output. There are lots more use cases to address if one is taking in memory arrays as input instead and we really don't have an intention at the moment to address them. If you want to propose changes along the lines of what you'd like to see please do. However, keep in mind that bioformats2raw is really only a few hundred lines of code. It may be substantially less work to implement something that is tailored to the imageplus --> Zarr workflow specifically.