From 4383ae5ff67e5ea984ee1fe88e26138056208e2b Mon Sep 17 00:00:00 2001 From: David Abramov Date: Tue, 25 Aug 2026 11:51:19 -0700 Subject: [PATCH 1/2] Patching ngff-zarr==0.39.0 to fix L0 clipping bug --- orchestration/flows/bl832/nersc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/orchestration/flows/bl832/nersc.py b/orchestration/flows/bl832/nersc.py index f5850a61..d1bac0b4 100644 --- a/orchestration/flows/bl832/nersc.py +++ b/orchestration/flows/bl832/nersc.py @@ -877,7 +877,7 @@ def build_multi_resolution( --volume {pscratch_path}/8.3.2:/alsdata \ --volume {pscratch_path}/8.3.2:/alsuser/ \ {multires_image} \ -bash -c "python tiff_to_zarr.py {recon_path} --raw_file {raw_path}" +bash -c "python -m pip install --user --no-deps 'ngff-zarr==0.39.0' && python tiff_to_zarr.py {recon_path} --raw_file {raw_path}" date """ From 17a1fb5dc929b3412fcee0a6bc79d2f7812ec562 Mon Sep 17 00:00:00 2001 From: David Abramov Date: Tue, 25 Aug 2026 11:52:10 -0700 Subject: [PATCH 2/2] pinning Zarr version in tiff_to_zarr.py --- scripts/perlmutter/tiff_to_zarr.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/perlmutter/tiff_to_zarr.py b/scripts/perlmutter/tiff_to_zarr.py index e07c6e0e..8a6de4fa 100644 --- a/scripts/perlmutter/tiff_to_zarr.py +++ b/scripts/perlmutter/tiff_to_zarr.py @@ -89,7 +89,7 @@ def main(): image.scale = read_pixelsize_from_hdf5(args.raw_file) image.axes_units = {'x': 'micrometer', 'y': 'micrometer', 'z': 'micrometer'} multiscales = to_multiscales(image, method=Methods.DASK_IMAGE_GAUSSIAN, cache=False) - to_ngff_zarr(zarr_dir, multiscales) + to_ngff_zarr(zarr_dir, multiscales, version="0.4") print('NGFF Zarr created') # Set permissions for the output directory and its contents