Invalid integer data type 'f'.

[will-moore]

I was hoping to concatenate some tiffs from https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1579 - I downloaded Brainiaqc_R1C1.zip and put the tiffs into a tiffs directory.

$ ls tiffs
ApoE.tiff			chan_144.tiff			FOXP3_nuc_include.tiff		IL13RA2.tiff
Au.tiff				chan_160.tiff			FOXP3.tiff			Ki67.tiff
...

Then tried to concatenate them across channels...

$ eubi to_zarr tiffs zarr_output --channel_tag ApoE,Au --concatenation_axes c --z_chunk 1

2025-08-04 11:40:05 - eubi_bridge.eubi_bridge.ebridge - INFO - Base conversion initiated.
2025-08-04 11:40:05 - eubi_bridge.eubi_bridge.ebridge - INFO - Verifying file extensions for distributed setup.
2025-08-04 11:40:05 - eubi_bridge.eubi_bridge.ebridge - INFO - File extensions were verified for distributed setup.
2025-08-04 11:40:05 - eubi_bridge.eubi_bridge.ebridge - INFO - 3.6 GB memory has been allocated per worker.
2025-08-04 11:40:05 - eubi_bridge.eubi_bridge.ebridge - INFO - Process running on local cluster.
SLF4J: No SLF4J providers were found.
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details.
SLF4J: No SLF4J providers were found.
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details.
2025-08-04 11:40:23 - eubi_bridge.eubi_bridge.ebridge - INFO - Metadata was extracted
2025-08-04 11:40:23 - eubi_bridge - CRITICAL - Uncaught exception
Traceback (most recent call last):
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/bin/eubi", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/eubi_bridge/cli.py", line 18, in main
    fire.Fire(EuBIBridge)
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/fire/core.py", line 135, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/fire/core.py", line 468, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
                                ^^^^^^^^^^^^^^^^^^^^
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/fire/core.py", line 684, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
                ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/eubi_bridge/ebridge.py", line 756, in to_zarr
    self.base_results = base.write_arrays(output_path,
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/eubi_bridge/ebridge_base.py", line 479, in write_arrays
    storage_results = store_arrays(
                      ^^^^^^^^^^^^^
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/eubi_bridge/base/writers.py", line 553, in store_arrays
    meta.add_channel(color = channel['color'],
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/eubi_bridge/ngff/multiscales.py", line 311, in add_channel
    max = np.iinfo(dtype).max
          ^^^^^^^^^^^^^^^
  File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/site-packages/numpy/_core/getlimits.py", line 707, in __init__
    raise ValueError(f"Invalid integer data type {self.kind!r}.")
ValueError: Invalid integer data type 'f'.

So I guess floating-point datatypes are not supported?

[bugraoezdemir]

@will-moore ,

This was a bug that was fixed in a recent version. Could you reinstall via:

# In the conda environment
pip install --no-cache-dir eubi-bridge==0.0.8b8
# Also reset the configuration:
eubi reset_config

This should normally solve the issue with floating point datatypes.

Just another point: your command would attempt to concatenate all images in the folder. If you only want to concatenate the images ApoE.tiff and Au.tiff, you can use wildcards like:

eubi to_zarr "tiffs/A*.tiff" zarr_output --channel_tag ApoE,Au --concatenation_axes c --z_chunk 1

Currently, the input files are not filtered with tags, but now I realize that it could actually make sense to do it that way.