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koenderinklab / OpenDDM

https://koenderinklab.github.io/OpenDDM/
Apache License 2.0
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Data handling #9

Closed mwakok closed 2 years ago

mwakok commented 2 years ago

Nice library for nd2: https://pypi.org/project/nd2/

iainmuntz commented 2 years ago

Looking at nd2 Running pims.open('file.nd2') works for nd2 files and (presumably) .tif files although these are not tested pims.open and nd2reader don't seem to find the frame rate, although they have other metadata such as pixels per micron opening .lif file is proving tricky as it seems to rely on java things

iainmuntz commented 2 years ago

I have implemented .nd2 files and .lif file handling, converting them to dask arrays with the same formatting for future analysis.

A note on .lif files is that they are 4 dimensional, as well as the usual x, y, t you also have 'series' as a dimension which lets you save multiple experiments in one file. I have not yet implemented a workaround for handling this so for the moment the read_lif function just reads in the first series