Michael SumnerFeb 16
explored a bunch of prominent #Zarr stores for accessibility, includes python tools for probing https://github.com/mdsumner/gdal-r-python/blob/main/zarr-examples/public-zarr-catalog/zarr_catalog.md - includes notes on (list in image)
Show threadPhilipp GärtnerJan 11

I added to "band_data" a '_CRS' attribute as dict with 'url', 'wkt' & 'projjson' infos (EPSG 3857), saved the whole thing as  file and hoped  can open it in  

However  seems to have trouble finding the coordinate reference and assumes the origin is 0,0 (Extent 0.0, -8192.0 : 4096.0, 0.0).

Now, my question: where do I store the "_CRS" dict correctly? Do I also need to add a GeoTransform infos? If yes, where?

2/2 #xarray #gdal #zarr

Philipp GärtnerJan 11

Sorry, that I misuse this platform for my silly question:

I have a  dataset
Dimensions: (time: 1, band: 4, y: 8192, x: 4096)
Coordinates:
* time datetime64[ns] 8B 2023-06-15
* band <U5 80B 'Red' 'Green' 'Blue' 'Alpha'
* y float32 33kB 7.064e+06 7.064e+06
* x float32 16kB 1.194e+06 1.194e+06
Data variables:
band_data (time, band, y, x) uint8 134MB dask.array<chunksize=(1, 4, 1024, 1024), meta=np.ndarray>
spatial_ref int64 8B ...

1/2 #xarray #gdal #zarr

NFDI4BIOIMAGENov 26

As part of the @NFDI4DS conference, @haesleinhuepf from @nfdi4bioimage gave a presentation on 'How LLMs impact BioImage Data Science', which is now available on #Zenodo. 🍁

The presentation slides provide information on using #LLMs for bioimage data science, based on various use cases such as image segmentation, feature extraction and UMAP creation, as well as opening a #Zarr file. The focus is on code generation for bioimage analysis.

👉 Click here for the slides: https://doi.org/10.5281/zenodo.17669681

Show threadPhilipp GärtnerNov 18

@jeremy beautiful, thanks. 🎉

#zarr
#xarray

Show threadPhilipp GärtnerNov 18
@jeremy useful to add #zarr #xarray emojis? 🙏 😀
Philipp GärtnerNov 18
There are many good examples of how to use the .zarr file format, but only a few examples of how to create a solid zarr (version 3) file from a bunch of .tif files. Who knows a good pipeline for #zarr creation? #cloud-native-geospatial #CNG
[email protected]Oct 15

📢Blosc2 3.10.2 Released! 📢

Building on the functions introduced in version 3.9, we have extended lazy evaluation to general expressions with ALL blosc2 functions in version 3.10.

Blosc2's compute engine ingests many array formats, as well as blosc2 arrays, with impressive results - see the graphic below!
Details on the comparisons in our blog: https://www.blosc.org/posts/tensordot-pure-persistent/

Blosc2's compute engine also powers Cat2Cloud (visit the demo site here https://cat2.cloud/demo/)!

#Zarr
#HDF5
#Python

Olivier D'Hondt 🛰️🌍🌱Oct 2
Figuring out the subtleties of using #Zarr to store complex numbers… I wish this was a bit more straightforward.
Olivier D'Hondt 🛰️🌍🌱Sep 25
#zarr or not #zarr, that is the question...