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image_portal_workflows
Workflows related to project previously referred to as "Hedwig"
BSD 3-Clause "New" or "Revised" License
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Consider adding more "secret" params to WF API
#380
philipmac
opened
11 months ago
5
Enable in-memory zarr rechunk (after updating tomojs-pytools) for czi related pipelines
#379
annshress
closed
11 months ago
0
Branch `feature/prefect2` PR's github action for test coverage is breaking
#378
annshress
closed
11 months ago
1
Breaking down czi_generate_imageset to multiple tasks
#377
annshress
closed
11 months ago
0
Use quantile based computations for CZI range
#376
blowekamp
closed
11 months ago
1
hot fix Quantiles parameters
#375
philipmac
closed
11 months ago
0
Upgrade prefect 1.* to 2.13
#374
annshress
closed
11 months ago
1
Remove dm and lrg-roi test input files from git
#373
annshress
closed
10 months ago
1
Decentralized test data
#372
annshress
closed
10 months ago
1
avoid using `/tmp` on compute
#371
philipmac
opened
11 months ago
1
Add missing copy workdir to assets for all workflows
#370
annshress
closed
11 months ago
0
Add omeXml: null in fileMetadata of all results
#368
annshress
closed
11 months ago
1
Null path in file metadata?
#367
sevaa
closed
11 months ago
12
Ignore this PR
#366
annshress
closed
12 months ago
0
Create util / wrapper that painlessly syncs large input files from S3 to local and vice versa
#365
philipmac
closed
10 months ago
1
Repo readme has aesthetic issues
#364
annshress
closed
11 months ago
1
The Label_image_sm was not generated for one of the HQ_image samples in QA
#363
NetaFG
closed
1 year ago
2
The multichannel pipeline parses at some cases the "scene#X_sm' thumbnail instead of the Image_label_sm
#362
NetaFG
closed
11 months ago
3
Return OME metadata xml file location along with ng metadata
#361
annshress
closed
1 year ago
1
prevents thumb gen for IF images
#360
philipmac
closed
1 year ago
1
Remove redundant return statement
#359
annshress
closed
1 year ago
1
add path to ome.xml to callback
#358
philipmac
closed
1 year ago
0
redundent jpeg seems to be being generated
#357
philipmac
closed
1 year ago
0
"View" links that are generated by the multichannel pipeline are lacking metadata
#356
NetaFG
closed
1 year ago
0
look at using subflows for big computes
#355
philipmac
closed
11 months ago
4
use flow_run_name in some useful way, eg input_dir
#354
philipmac
closed
10 months ago
1
Feature: Upgrade prefect 1.* to 2.13
#353
annshress
closed
11 months ago
1
Prevent users from submitting H&E CZI input files to IF pipeline
#352
philipmac
opened
1 year ago
0
label image incorrectly oriented
#351
philipmac
closed
1 year ago
0
hardcode in XY for API
#350
philipmac
closed
1 year ago
1
GUI does not want to recieve XYC dims in callback
#349
philipmac
closed
1 year ago
0
Rotate label image 90 clock wise
#348
blowekamp
closed
1 year ago
1
Mad scale
#347
blowekamp
closed
1 year ago
1
One out of the 8 PNG files failed during the run
#346
NetaFG
closed
1 year ago
1
Change locations for zarr image in single image workflows
#345
annshress
closed
1 year ago
1
Update shader parameters spec to include XYC dimensions
#344
blowekamp
closed
1 year ago
1
for single image workflows - eg BRT / large PNG / SEM - check location of image in zarr structure
#343
philipmac
closed
1 year ago
0
update SEM neuroglancer metadata to new format
#342
philipmac
closed
1 year ago
0
use pytools wheel
#341
philipmac
closed
1 year ago
1
Swap to pytools wheel
#340
annshress
closed
1 year ago
0
Fix/update brt ng metadata
#339
philipmac
closed
1 year ago
1
update BRT Neuroglancer to new format
#338
philipmac
closed
1 year ago
1
Bumps to pytools 3.0b02
#337
philipmac
closed
1 year ago
1
Refactor ng_gen_metadata to use pytools.HedwigZarrImage(s) objects
#336
annshress
closed
1 year ago
0
Callback output can be written to an output file
#335
annshress
closed
1 year ago
1
Fixes the removal of `scale-string-format` argument from bioformats2raw
#334
annshress
closed
1 year ago
1
Fix gen_zarr mock function
#333
annshress
closed
11 months ago
1
gen zarr failing
#332
philipmac
closed
1 year ago
0
removing --scale-format-string from bioformats command
#331
philipmac
closed
1 year ago
1
remove --scale-format-string arg from bioformats2raw conversion
#330
philipmac
closed
1 year ago
0
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