search

bioio-devs / bioio-sldy

A BioIO reader plugin for reading 3i slidebook (SLDY) images
BSD 3-Clause "New" or "Revised" License
0 stars 0 forks source link

Please add ability to read `.sld` files (note these are not the same as `.sldy` files) #17

Open SergeEParent opened 1 month ago

SergeEParent commented 1 month ago

Feature Description

Could you please add the ability for bioio-sldy to work with .sld files (note that these are different from .sldy files). This is currently blocking us from working with some data.

Use Case

To load image data from very large .sld files as a dask array so that we can do further analysis on the data.

Solution

An implementation similar to how we currently work with .sldy, .czi, and .nd2 files.

Alternatives

My apologies but I don't know enough about how the bioio-sldy plugin works to provide an alternative.

toloudis commented 1 month ago

I wonder if this should be a separate bioio-sld plugin.

@SergeEParent Will you be using both sld and sldy on a regular basis?

toloudis commented 1 month ago

Also, as a near term workaround I wonder if you can use bioio-bioformats as the reader?

SergeEParent commented 1 month ago

@toloudis We were hoping to use .sld files more regularly since the experimentalists collecting the data find those file types easier to work with and the data is originally collected as a .sld (by necessity). Since I originally posted this feature request we found that we could save a copy of the .sld as a .sldy and work with that so we are no longer blocked, but it will increase the space used on Vast which I know is a valuable resource.

toloudis commented 1 month ago

Ok good to know you aren't blocked. I suggest in the near term seeing if the bioformats-reader will work. im = BioImage(path_to_sld, reader=bioio_bioformats.Reader)