Test labels ZarrReader

[will-moore]

As discussed in today's IDR meeting, each idr0138 image should be represented in OME-NGFF spec as a single image, rather than 3 images that includes labels. This is what ZarrReader should read and it should be imported into OMERO as a single-image Fileset.

Testing today's ZarrReader... updated on idr-testing as at ome/ZarrReader#64 (comment)

On idr-testing:omeroreadwrite as omero-server
Make a copy of Image so we can compare import with/without chunks...
First, import with chunks...

cd /opt/omero/server
mkdir -p idr0138/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/
cd idr0138/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/
cp -R /uod/idr/filesets/idr0138-lohoff-seqfish/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr ./
$ omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231106.log --errs /tmp/idr0138_20231106.err 

...
2023-11-06 15:25:50,138 368382     [3-thread-1] INFO   s.importer.transfers.SymlinkFileTransfer - Transferring /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/4/1/1/0/0...
2023-11-06 15:25:50,223 368467     [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/4/1/1/0/0
2023-11-06 15:25:51,377 369621     [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/4/1/1/0/0
2023-11-06 15:26:00,078 378322     [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2023-11-06 15:26:00,200 378444     [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 61519389
2023-11-06 15:26:01,296 379540     [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 61519389
2023-11-06 15:26:01,730 379974     [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 61519389
2023-11-06 15:26:01,768 380012     [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 61519389
2023-11-06 15:26:01,821 380065     [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 61519389
2023-11-06 15:26:01,861 380105     [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 61519389
2023-11-06 15:26:02,026 380270     [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/1/0/0/2/2
Other imported objects:
Fileset:6314643

==> Summary
655 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:06:16.467

Imports as a single image as expected:

Now lets delete chunks from the image and re-import...

$ find . -type f -name 0 -delete
$ find . -type f -name 1 -delete
$ find . -type f -name 2 -delete
$ find . -type f -name 3 -delete

omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231106nc.log --errs /tmp/idr0138_20231106nc.err 

...
2023-11-06 15:40:21,260 287        [      main] INFO          ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.7.1
2023-11-06 15:40:21,280 307        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 7.0.0 revision: 3f8b3326cb578d59bd948fb84c838ff77e9f1b08 date: 1 August 2023
2023-11-06 15:40:21,354 381        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64
2023-11-06 15:40:21,355 382        [      main] INFO   formats.importer.cli.CommandLineImporter - Skipping thumbnails creation
2023-11-06 15:40:21,355 382        [      main] INFO   formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation
2023-11-06 15:40:21,355 382        [      main] INFO   formats.importer.cli.CommandLineImporter - Disabling upgrade check
2023-11-06 15:40:21,355 382        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2023-11-06 15:40:21,358 385        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2023-11-06 15:40:21,722 749        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 100 Metadata Level: MINIMUM
2023-11-06 15:40:21,732 759        [      main] INFO      ome.formats.importer.ImportCandidates - 23 file(s) parsed into 0 group(s) with 0 call(s) to setId in 0ms. (10ms total) [0 unknowns]
2023-11-06 15:40:21,777 804        [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2023-11-06 15:40:22,329 1356       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2023-11-06 15:40:22,691 1718       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.
2023-11-06 15:40:22,701 1728       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.6.9
2023-11-06 15:40:22,701 1728       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.7.1
2023-11-06 15:40:22,701 1728       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.20
2023-11-06 15:40:22,701 1728       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2023-11-06 15:40:22,701 1728       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2023-11-06 15:40:22,701 1728       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 3.10.0-1160.99.1.el7.x86_64
No imports found

Hmmm 👎

[will-moore]

Try different deletion method to get a no-chunks image...

Make another copy of the image as above, then...

(venv3) bash-4.2$ rm -rf MMStack_Pos0.ome.zarr/0/0
(venv3) bash-4.2$ rm -rf MMStack_Pos0.ome.zarr/0/2
(venv3) bash-4.2$ rm -rf MMStack_Pos0.ome.zarr/0/1
(venv3) bash-4.2$ rm -rf MMStack_Pos0.ome.zarr/0/3
(venv3) bash-4.2$ rm -rf MMStack_Pos0.ome.zarr/0/4
omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231106nc2.log --errs /tmp/idr0138_20231106nc2.err

...
2023-11-06 15:56:42,438 156117     [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/4/1/1/0/0
2023-11-06 15:56:46,262 159941     [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2023-11-06 15:56:46,348 160027     [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 61520188
2023-11-06 15:56:47,219 160898     [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 61520188
2023-11-06 15:56:47,578 161257     [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 61520188
2023-11-06 15:56:47,612 161291     [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 61520188
2023-11-06 15:56:47,658 161337     [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 61520188
2023-11-06 15:56:47,692 161371     [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 61520188
2023-11-06 15:56:47,847 161526     [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/1/0/0/2/2
Other imported objects:
Fileset:6314644

==> Summary
271 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:02:38.611

Faster import - in 2:38 mins instead of 6:16 - but I only deleted chunks from highest resolution.

EDIT....
Viewing this image fails...

    serverExceptionClass = ome.conditions.ResourceError
    message = Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-0/2023-11/06/15-54-09.739/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/1/0/0/2/2

Blitz log:

2023-11-07 11:14:51,598 ERROR [         ome.io.bioformats.BfPixelBuffer] (l.Server-4) Failed to instantiate BfPixelsWrapper with /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-0/2023-11/06/15-54-09.739/ngff/TimEmbr
yos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/1/0/0/2/2
2023-11-07 11:14:51,599 ERROR [                ome.io.nio.PixelsService] (l.Server-4) Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-0/2023-11/06/15-54-09.739/ngff/TimEmbryos-10221
9/HybCycle_0/MMStack_Pos0.ome.zarr/1/0/0/2/2
java.lang.RuntimeException: java.io.FileNotFoundException: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-0/2023-11/06/15-54-09.739/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/1/0/0/2/2 (No such file or
 directory)
        at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:79)
        at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:124)

This MMStack_Pos0.ome.zarr/1/ wasn't the dir that was deleted above, but it is a symlink to the data that I deleted below!

...end EDIT.

Deleted chunks from other resolutions...

rm -rf MMStack_Pos0.ome.zarr/1/0
rm -rf MMStack_Pos0.ome.zarr/1/1
rm -rf MMStack_Pos0.ome.zarr/1/2
rm -rf MMStack_Pos0.ome.zarr/1/3
rm -rf MMStack_Pos0.ome.zarr/1/4
rm -rf MMStack_Pos0.ome.zarr/2/0
rm -rf MMStack_Pos0.ome.zarr/2/1
rm -rf MMStack_Pos0.ome.zarr/2/2
rm -rf MMStack_Pos0.ome.zarr/2/3
rm -rf MMStack_Pos0.ome.zarr/3/4
rm -rf MMStack_Pos0.ome.zarr/3/0
rm -rf MMStack_Pos0.ome.zarr/3/1
rm -rf MMStack_Pos0.ome.zarr/4/   -- oops - made another copy of this dir and then...
rm -rf MMStack_Pos0.ome.zarr/4/0
rm -rf MMStack_Pos0.ome.zarr/4/1

omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231106nc3.log --errs /tmp/idr0138_20231106nc3.err

2023-11-06 16:01:33,912 275        [      main] INFO          ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.7.1
2023-11-06 16:01:33,931 294        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 7.0.0 revision: 3f8b3326cb578d59bd948fb84c838ff77e9f1b08 date: 1 August 2023
2023-11-06 16:01:33,995 358        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64
2023-11-06 16:01:33,996 359        [      main] INFO   formats.importer.cli.CommandLineImporter - Skipping thumbnails creation
2023-11-06 16:01:33,996 359        [      main] INFO   formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation
2023-11-06 16:01:33,996 359        [      main] INFO   formats.importer.cli.CommandLineImporter - Disabling upgrade check
2023-11-06 16:01:33,996 359        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2023-11-06 16:01:33,999 362        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2023-11-06 16:01:34,371 734        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 100 Metadata Level: MINIMUM
2023-11-06 16:01:34,397 760        [      main] ERROR                loci.formats.FormatHandler - ZarrReader loaded options file from: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr
2023-11-06 16:01:34,748 1111       [      main] ERROR                loci.formats.FormatHandler - ZarrReader loaded options file from: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr
2023-11-06 16:01:34,749 1112       [      main] ERROR                loci.formats.FormatHandler - ZarrReader getUsed files, skipPixels: false
2023-11-06 16:01:34,749 1112       [      main] ERROR                loci.formats.FormatHandler - ZarrReader fetching list of used files: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr
2023-11-06 16:01:34,752 1115       [      main] ERROR                loci.formats.FormatHandler - Adding to the used files list: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/.zattrs
...
2023-11-06 16:01:35,073 1436       [      main] ERROR                loci.formats.FormatHandler - Adding to the used files list: /opt/omero/server/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/4/.zarray
2023-11-06 16:01:35,075 1438       [      main] INFO      ome.formats.importer.ImportCandidates - 48 file(s) parsed into 0 group(s) with 25 call(s) to setId in 687ms. (704ms total) [0 unknowns]
2023-11-06 16:01:35,127 1490       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2023-11-06 16:01:35,688 2051       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2023-11-06 16:01:36,081 2444       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.
2023-11-06 16:01:36,097 2460       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.6.9
2023-11-06 16:01:36,097 2460       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.7.1
2023-11-06 16:01:36,097 2460       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.20
2023-11-06 16:01:36,097 2460       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2023-11-06 16:01:36,097 2460       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2023-11-06 16:01:36,097 2460       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 3.10.0-1160.99.1.el7.x86_64
No imports found

Strange! Seems like deleting some chunks is OK, but deleting all is not.

[will-moore]

From above, deleting highest resolutions chunks is OK (still importable), but deleting too much failed.

Let's try a bunch of imports... 'A', 'B' etc..

Start with fresh copy of image above.. as omero-server...

cd
cd idr0138
mkdir A && cd A
cp -R /uod/idr/filesets/idr0138-lohoff-seqfish/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr ./

$ rm -rf MMStack_Pos0.ome.zarr/0/0
$ rm -rf MMStack_Pos0.ome.zarr/0/2
$ rm -rf MMStack_Pos0.ome.zarr/0/1
$ rm -rf MMStack_Pos0.ome.zarr/0/3
$ rm -rf MMStack_Pos0.ome.zarr/0/4

omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231107A.log --errs /tmp/idr0138_20231107A.err
...
Fileset:6314646
==> Summary
271 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:02:37.761

Image is viewable and only 'black' at highest resolution. 👍

Let's copy that image and delete all chunk dirs under 2nd resolution...

mkdir B && cd B
cp -R ../A/MMStack_Pos0.ome.zarr ./
rm -rf MMStack_Pos0.ome.zarr/1/0
rm -rf MMStack_Pos0.ome.zarr/1/1
rm -rf MMStack_Pos0.ome.zarr/1/2
rm -rf MMStack_Pos0.ome.zarr/1/3
$ omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231107B.log --errs /tmp/idr0138_20231107B.err
...
Fileset:6314647
==> Summary
79 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:00:58.923

Repeat for C

mkdir C && cd C
$ cp -R ../B/MMStack_Pos0.ome.zarr ./
rm -rf MMStack_Pos0.ome.zarr/2/0
rm -rf MMStack_Pos0.ome.zarr/2/1
rm -rf MMStack_Pos0.ome.zarr/2/2
rm -rf MMStack_Pos0.ome.zarr/2/3
$ omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231107C.log --errs /tmp/idr0138_20231107C.err
...
Fileset:6314648
==> Summary
31 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:00:22.762

And D...

mkdir D && cd D
$ cp -R ../C/MMStack_Pos0.ome.zarr ./
rm -rf MMStack_Pos0.ome.zarr/3/0
rm -rf MMStack_Pos0.ome.zarr/3/1
omero import -d 18251 --transfer=ln_s --skip=all --depth=100 MMStack_Pos0.ome.zarr --file /tmp/idr0138_20231107D.log --errs /tmp/idr0138_20231107D.err
...
2023-11-07 11:59:07,998 1453       [      main] ERROR                loci.formats.FormatHandler - Adding to the used files list: /opt/omero/server/idr0138/D/MMStack_Pos0.ome.zarr/labels/cells/4/0/0/0
2023-11-07 11:59:08,000 1455       [      main] INFO      ome.formats.importer.ImportCandidates - 56 file(s) parsed into 0 group(s) with 26 call(s) to setId in 682ms. (702ms total) [0 unknowns]
2023-11-07 11:59:08,046 1501       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2023-11-07 11:59:08,580 2035       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2023-11-07 11:59:08,927 2382       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.
2023-11-07 11:59:08,941 2396       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.6.9
2023-11-07 11:59:08,942 2397       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.7.1
2023-11-07 11:59:08,942 2397       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.20
2023-11-07 11:59:08,942 2397       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2023-11-07 11:59:08,942 2397       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2023-11-07 11:59:08,942 2397       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 3.10.0-1160.99.1.el7.x86_64
No imports found

Strange! Deleting those 2 chunk dirs from MMStack_Pos0.ome.zarr/3/ made the difference between importing OK and failing!

Now we need to update symlinks for A, B, C above...

python idr-utils/scripts/managed_repo_symlinks.py Image:15148937 /uod/idr/filesets/idr0138-lohoff-seqfish/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/ --repo /data/OMERO/ManagedRepository --report

This failed as we have extra /server/idr0138/
Do it manually...

rm -rf /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-5/2023-11/07/11-55-17.605/server/idr0138/C/MMStack_Pos0.ome.zarr

ln -s /uod/idr/filesets/idr0138-lohoff-seqfish/20210917-Globus/ngff/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-5/2023-11/07/11-55-17.605/server/idr0138/C/MMStack_Pos0.ome.zarr

$ ls -alh /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-5/2023-11/07/11-55-17.605/server/idr0138/C/MMStack_Pos0.ome.zarr/
total 40K
drwxrwx---.  8 idrftp microarray 4.0K Jun 15  2022 .
drwxrwx---. 53 idrftp microarray 8.0K Jun 15  2022 ..
drwxrwx---.  6 idrftp microarray 4.0K Jun 15  2022 0
drwxrwx---.  6 idrftp microarray 4.0K Jun 15  2022 1
drwxrwx---.  6 idrftp microarray 4.0K Jun 15  2022 2
drwxrwx---.  4 idrftp microarray 4.0K Jun 15  2022 3
drwxrwx---.  4 idrftp microarray 4.0K Jun 15  2022 4
drwxrwx---.  4 idrftp microarray 4.0K Jun 15  2022 labels
-rw-rw----.  1 idrftp microarray 3.0K Jun 16  2022 .zattrs
-rw-rw----.  1 idrftp microarray   24 Jun 16  2022 .zgroup

This allows us to load chunks for all resolution levels...

[will-moore]

Importing without chunks and updating symlink does result in a much faster import (22 secs instead of 6 mins) but tricky steps:

• make a copy of every Image
• delete some chunks, but not too many!
• Update https://github.com/IDR/idr0138-lohoff-seqfish/blob/main/experimentA/idr0138-experimentA-filePaths.tsv to point to copies
• Do the import
• Update symlinks (could use managed_repo_symlinks.py script once ZarrReader performance improvements ome/ZarrReader#64 (comment) is fixed).

Too many unknowns. Probably not worth attempting this at this stage.
Stick with regular import (approx 2 weeks).