Auto-Minerva unable to process Coreograph output

[ArtemSokolov]

Presently, Auto-Minerva expects a pyramid OME-TIFF, while Coreograph produces flat .tif files.

To fix: Option 1: Allow Auto-Minerva to process small pyramid-free images, such as the ones produced by Coreograph Option 2: Update Coreograph to produce pyramid OME-TIFF files

[hengkp]

Hi @ArtemSokolov,

I came from the #72187 After run this command:

nextflow run labsyspharm/mcmicro --in /sisplockers/MCMICRO/exemplar-002 --viz --segmentation ilastik

It shows an error as you have mentioned as follows:

N E X T F L O W ~ version 22.04.5 Launching https://github.com/labsyspharm/mcmicro [exotic_wozniak] DSL2 - revision: 1472f63a5c [master] executor > local (22) [- ] process > illumination - [12/457d92] process > registration:ashlar [100%] 1 of 1 ✔ [c1/d41aa8] process > dearray:coreograph (1) [100%] 1 of 1 ✔ [- ] process > segmentation:roadie:runTask - executor > local (22) [- ] process > illumination - [12/457d92] process > registration:ashlar [100%] 1 of 1 ✔ [c1/d41aa8] process > dearray:coreograph (1) [100%] 1 of 1 ✔ [- ] process > segmentation:roadie:runTask - [a7/d06a56] process > segmentation:worker (ilasti... [100%] 4 of 4 ✔ [0e/67b4ff] process > segmentation:s3seg (2) [100%] 4 of 4 ✔ [6d/e5dd52] process > quantification:mcquant (3) [ 0%] 0 of 1 [- ] process > downstream:worker - [c5/a08e0a] process > viz:roadie:runTask (1) [100%] 3 of 3 [e6/ad177e] process > viz:autominerva (1) [ 33%] 1 of 3, failed: 1 [1d/81d04b] process > provenance [100%] 1 of 1 ✔ Error executing process > 'viz:autominerva (1)'

Caused by: Process viz:autominerva (1) terminated with an error exit status (1)

Command executed:

python /app/minerva-author/src/save_exhibit_pyramid.py 3.tif 3.json 3

Command exit status: 1

Command output: (empty)

Command error: Traceback (most recent call last): File "/app/minerva-author/src/save_exhibit_pyramid.py", line 209, in main(ome_tiff, author_json, output_dir, root_url, vis_dir, force) File "/app/minerva-author/src/save_exhibit_pyramid.py", line 152, in main exhibit_config = make_exhibit_config(opener, root_url, saved) File "/app/minerva-author/src/save_exhibit_pyramid.py", line 84, in make_exhibit_config (num_channels, num_levels, width, height) = opener.get_shape() TypeError: cannot unpack non-iterable NoneType object

Work dir: /home/nodeadmin/work/e6/ad177e3a424332735287e818c4c439

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

Also, for the log file:

cat /home/nodeadmin/work/e6/ad177e3a424332735287e818c4c439/.command.log

Traceback (most recent call last): File "/app/minerva-author/src/save_exhibit_pyramid.py", line 209, in main(ome_tiff, author_json, output_dir, root_url, vis_dir, force) File "/app/minerva-author/src/save_exhibit_pyramid.py", line 152, in main exhibit_config = make_exhibit_config(opener, root_url, saved) File "/app/minerva-author/src/save_exhibit_pyramid.py", line 84, in make_exhibit_config (num_channels, num_levels, width, height) = opener.get_shape() TypeError: cannot unpack non-iterable NoneType object

I see you suggest two options, but I am unsure how to perform them. Please advice.

Thanks, Heng

[ArtemSokolov]

Hi Heng,

Just a small update:

• We have been able to reproduce your issue with UnMicst in another environment and are in the process of debugging now.
• The two options are proposals for future development. After some discussion, we are going to pursue option 2 and will try to implement a solution soon.

Best, -Artem