Reading in non-CZI data

m-albert / MVRegFus

Python module for registering and fusing multi-view microscopy data

BSD 3-Clause "New" or "Revised" License

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Reading in non-CZI data #6

Open dpshepherd opened 3 years ago

dpshepherd commented 3 years ago

We also have a second, but separate question. We typically save our data as TIFFs and then convert to the BigDataViewer (BDV) H5 format, using npy2bdv. Since we can read our data in as NumPy or a Dask array, we are also curious if you could give a hint for the hooks where can feed data into the registration and fusion routine that are not CZI files?

Thanks! Doug

m-albert commented 3 years ago

Definitely converging on a good way to flexibly read non-CZI data is high up on the priority list!

Currently the workflow on master assumes a single czi input file. As mentioned in https://github.com/m-albert/MVRegFus/issues/5#issuecomment-732511787, experimentally the tif_input branch can deal with tif input data as exemplified in this notebook. Parameters such as the physical spacing and origin can be provided manually.