Sébastien Besson

Hi @Cumol, the Bio-Formats command-line tools and more generally `IFormatReader.setId` method is expecting a file as the input and will not handle directories as suggested by the exception. Converting Metamorph...

@BioinfoTongLI `bioformats2raw` uses the `S3FileSystemProvider` implementation from the `org.lasersonlab:s3fs` library to write to S3. The URI specification is described in https://github.com/lasersonlab/Amazon-S3-FileSystem-NIO2 and is epxected to be of the form `s3://s3-.amazonaws.com//`...

The error tells you the command is unable to find the `spatial_demo_datasets` bucket. What happens if you remove`s3-us-east-1` from the URI as these are very AWS S3 specific- see https://docs.aws.amazon.com/general/latest/gr/s3.html....

I don't think there is any retry on error logic. Does the above happen for every tile? Or randomly?

See https://github.com/aws/aws-sdk-java/issues/1212, it looks like others are facing a similar issue as yours. Based on this thread, it might be worth trying to increase the maximum number of retry attempts...

> and I believe the retry time is arbitary depends on server load? That's what the linked issue suggests. It feels plausible but you would need the server logs to...

Closing this as the original issue was addressed. As per the latest comment, the investigation has now progressed into tuning the available parameters for optimizing the write to the object...

For reference the [migration guide](https://numpy.org/doc/stable/numpy_2_0_migration_guide.html) has been published. Learning from the NumPy 2.0.0 story, I suspect the next iteration should probably be `numpy `numpy

For reference, as we were starting to look into Python 3.13, came across https://numpy.org/devdocs/release/2.1.0-notes.html#numpy-2-1-0-release-notes ``` NumPy 2.1.0 provides support for the upcoming Python 3.13 release and drops support for Python...

https://pypi.org/project/omero-py/5.20.0/ was released earlier today with the constraint relaxation to support NumPy 1.x and NumPy 2.x