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niaid / image_portal_workflows

Workflows related to project previously referred to as "Hedwig"
BSD 3-Clause "New" or "Revised" License
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run OME TIFF through CZI processsing pipeline #431

Closed philipmac closed 6 months ago

philipmac commented 7 months ago

motivation - test for image registration OME itffs can be found: "ai-rmlsbatch1:/mnt/ai-fas12/RMLEMHedwigQA/TestData/Nanostringfiles/ROI\ Alignment\ Images\ for\ Brad"

philipmac commented 6 months ago

shader params:

"metadata": {"shader": "MultiChannel", "dimensions": "XY", "shaderParameters": {"brightness": 0.0, "contrast": 0.0, "channelArray": [{"range": [1, 17579], "window": [0, 43049], "name": "fitc_525nm", "color": "red", "channel": 0, "clamp": false, "enabled": true}, {"range": [19, 1139], "window": [0, 4199], "name": "cy3_568nm", "color": "green", "channel": 1, "clamp": false, "enabled": true}, {"range": [11, 3977], "window": [0, 29093], "name": "texas_red_615nm", "color": "blue", "channel": 2, "clamp": false, "enabled": true}, {"range": [79, 12381], "window": [0, 32297], "name": "cy5_666nm", "color": "cyan", "channel": 3, "clamp": false, "enabled": true}]}}}]}]

philipmac commented 6 months ago

input file: /gs1/home/hedwig_dev/image_portal_workflows/test/input_files/IF_czi/Projects/tiff_input

6.9G Jan 30 12:01 IA_P2_S2.ome.tiff

timings: bioformats2raw command 13:52:27 -> 13:53:20

rechunk_zarr-0' - Task took 53.152 seconds

INFO:pytools.HedwigZarrImage:Building histogram for "/gs1/home/hedwig_dev/image_portal_workflows/test/input_files/IF_czi/Assets/tiff_input/IA_P2_S2.ome/IA_P2_S2.ome.zarr/0"... 13:59:38.882 | INFO | pytools.HedwigZarrImage - Building histogram for "/gs1/home/hedwig_dev/image_portal_workflows/test/input_files/IF_czi/Assets/tiff_input/IA_P2_S2.ome/IA_P2_S2.ome.zarr/0"... INFO:pytools.HedwigZarrImage:Computing statistics... 14:00:01.561 | INFO | pytools.HedwigZarrImage - Computing statistics... DEBUG:pytools.HedwigZarrImage:stats: {'median': 0.2784014669350374, 'mad': 0.4017881802869134, 'mean': 511.5731216542423, 'var': 2545527.7462718966, 'sigma': 1595.471010790198, 'min': 0.0, 'max': 65535.0, 'quantiles': {0.01: 79.14563185737383, 0.99: 12380.091587332423, 0.9999: 32296.226399999978}} 14:00:01.567