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niaid
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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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Some 16bit Tiff files show black after running the 2D pipeline in Prod
#278
NetaFG
closed
1 year ago
7
Config modifications
#277
annshress
closed
1 year ago
4
Taking configs out of the source code
#276
annshress
closed
1 year ago
3
Code in containers
#275
annshress
closed
1 year ago
6
conform to new callback format
#274
philipmac
closed
1 year ago
0
use max num_workers on bioformats2raw
#273
philipmac
closed
1 year ago
0
update GHA to run python v3.10
#272
philipmac
opened
1 year ago
0
check imod installation (is spack?)
#271
philipmac
closed
11 months ago
1
document how to use git LFS better
#270
philipmac
closed
10 months ago
1
Script to extract a czi "macro images" to a thumbnail
#269
blowekamp
closed
1 year ago
0
Update hpc.rst
#268
philipmac
closed
1 year ago
0
adding explanations of file layout for spatial omics set up.
#267
philipmac
closed
1 year ago
0
Correct legacy example for metadata
#266
blowekamp
closed
1 year ago
0
Add count of produced outputs to end-to-end tests
#265
mbopfNIH
opened
1 year ago
2
Removed "shortcut" code from BRT test.
#264
mbopfNIH
closed
1 year ago
0
Remove "shortcut" version of BRT test
#263
mbopfNIH
closed
1 year ago
1
Update metadata.yml for float brightness and contrast
#262
blowekamp
closed
1 year ago
0
adding illustrative example of proposed callback
#261
philipmac
closed
1 year ago
1
Add samples of new metadata json to be produced by the pipeline
#260
blowekamp
closed
1 year ago
0
Added bioformats2raw to GH build and added tests.
#259
mbopfNIH
closed
1 year ago
0
Bump slurm walltime
#258
philipmac
closed
1 year ago
0
SEM-Tomo pipeline has been running for more than 7 hours in QA - 7/5/2023
#257
NetaFG
closed
1 year ago
7
Pipeline runs are held in "scheduled status" on the Prefect UI - 6/30/2023
#256
NetaFG
closed
1 year ago
1
2D pipeline failed in QA - 6/30/2023
#255
NetaFG
closed
1 year ago
1
adds keyImage, closes #253
#254
philipmac
closed
1 year ago
0
add keyImage to large PNG -> zarr pipeline
#253
philipmac
closed
1 year ago
0
tells setup to install templates, fixes #250
#252
philipmac
closed
1 year ago
0
Lrg 2d rgb pipeline
#251
philipmac
closed
1 year ago
1
Two BRT pipeline runs failed in Dev
#250
NetaFG
closed
1 year ago
2
are (unused?) alpha channels in large png files intended?
#249
philipmac
closed
1 year ago
2
adds more details about HPC setup
#248
philipmac
closed
1 year ago
0
The 2D pipeline failed in Dev on 6/19/2023
#247
NetaFG
closed
1 year ago
1
Update hpc.rst
#246
philipmac
closed
1 year ago
0
Hpc install mods
#245
philipmac
closed
1 year ago
0
Formulate the COE list for the Hedwig pipeline
#241
NetaFG
closed
1 year ago
2
GitHub Actions run of pytest has problems
#240
mbopfNIH
opened
1 year ago
2
Made modifications to upgrade to Prefect2
#239
mbopfNIH
closed
1 year ago
1
Run error in Prod - 2D pipeline - 7/6/2023
#238
NetaFG
closed
1 year ago
3
Prototype upgrading to Prefect2
#237
mbopfNIH
closed
1 year ago
9
Run error in Prod from 6/2/2023
#236
NetaFG
closed
1 year ago
2
thumbnail generation - qual too low, bump to 90
#235
philipmac
closed
1 year ago
2
Run error in QA from 5/26/2023
#234
NetaFG
closed
1 year ago
1
Hpc fixes
#233
philipmac
closed
1 year ago
3
Fixed typo in __str__ method
#232
mbopfNIH
closed
1 year ago
0
Added environment variable switch to run complete BRT test
#231
mbopfNIH
closed
1 year ago
2
Toggle `test_brt` shortcut mode from command line
#230
mbopfNIH
closed
1 year ago
3
Using pytest.mark to tag tests
#229
mbopfNIH
closed
1 year ago
5
Create method to run different classes of test
#228
mbopfNIH
closed
1 year ago
0
Remove dead code and increase test coverage
#226
mbopfNIH
closed
1 year ago
1
Flake8 fails with "W605 invalid escape sequence"
#225
mbopfNIH
closed
1 year ago
1
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