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dchaley
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deepcell-imaging
Tools & guidance to scale DeepCell imaging on Google Cloud Batch
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Implement segment and measure job
#315
dchaley
closed
9 hours ago
0
Container & other settings have to come from config or params
#314
dchaley
opened
9 hours ago
0
Don't create segment job gather-benchmark tasks if the BigQuery table is blank
#313
dchaley
opened
1 day ago
0
Add script to enqueue QuPath job
#312
dchaley
closed
2 days ago
0
Create runnable for submitting downstream job on completion
#311
dchaley
closed
2 days ago
0
Update README to share batch benchmark results
#310
langitlynn
opened
4 days ago
1
Use blanks for strings, optional for image_mpp
#309
dchaley
closed
6 days ago
0
VULNs: Can we update TF?
#308
dchaley
opened
6 days ago
0
Remove optionals; update pipeline.sh to have benchmarks
#307
dchaley
closed
6 days ago
0
Fix broken optional arguments
#306
dchaley
closed
6 days ago
0
Increase boot disk size based on input size
#305
dchaley
opened
1 week ago
1
Create fresh StringIO on each BQ upload
#304
dchaley
closed
1 week ago
0
Recreate StringIO on each BQ upload try
#303
dchaley
closed
1 week ago
0
Move to src layout & use requirements for project dependencies
#302
dchaley
closed
2 weeks ago
0
Update QuPath job to run multiple predictions
#301
dchaley
closed
2 weeks ago
0
Generated command-line arguments
#300
dchaley
closed
2 weeks ago
0
Accept indexed task args
#299
dchaley
closed
2 weeks ago
0
Split tiff output by compartment
#298
dchaley
opened
3 weeks ago
0
Add user-project parameters to storage interactions
#297
dchaley
opened
3 weeks ago
0
Add new benchmark with just gs_fastcopy
#296
dchaley
closed
3 weeks ago
0
Add benchmark for just gs_fastcopy
#295
dchaley
closed
3 weeks ago
0
Create QuPath segment + measure job
#294
dchaley
opened
3 weeks ago
3
Create job that runs qupath creation script on a dataset root
#293
dchaley
closed
4 days ago
7
Create job that processes multiple inputs
#292
dchaley
closed
2 weeks ago
1
Add savez_compressed download + more explanation
#291
dchaley
closed
4 weeks ago
0
Add WIP template for sending Teams notifications
#290
dchaley
closed
4 weeks ago
0
Pass compartment from runner to job json
#289
dchaley
closed
4 weeks ago
0
Add benchmarking script: smart_open / gs_fastcopy
#288
dchaley
closed
1 month ago
0
Add benchmark for serial smart_open vs parallel gs_fastcopy transfers
#287
dchaley
closed
3 weeks ago
1
Get batch configuration fields from config file
#286
dchaley
closed
1 month ago
2
Need to thread compartment through parameters
#285
dchaley
closed
4 weeks ago
0
Add parameter for batch job configuration
#284
dchaley
closed
1 month ago
0
Add a Teams-formatted webhook call on pipeline success
#283
dchaley
opened
1 month ago
3
Add qupath runner
#282
dchaley
closed
1 month ago
0
Add script to run DeepCell with QuPath conventions
#281
dchaley
closed
1 month ago
5
Move GCP JSON formatter to root & remove other handlers
#280
dchaley
closed
1 month ago
0
Log entries are duplicated
#279
dchaley
closed
1 month ago
0
Use JSON logging
#278
dchaley
closed
1 month ago
0
Use renamed h5 not .keras (it's actually hdf5)
#277
dchaley
closed
1 month ago
0
Use HDF5 format
#276
dchaley
closed
1 month ago
2
Multi-step job: write tiff using input file basename
#275
dchaley
closed
1 month ago
0
Output tiffs as int32 in benchmark + multistep
#274
dchaley
closed
1 month ago
0
Consider including TF model on Docker container
#273
dchaley
opened
1 month ago
0
Use container tag batch not gce
#272
dchaley
closed
1 month ago
0
Bug: run-job scripts using wrong container tag
#271
dchaley
closed
1 month ago
0
Add model_path and model_hash arguments to run-multistep-job
#270
dchaley
closed
1 month ago
0
Bring multi-step to parity with benchmark.py
#269
dchaley
closed
1 month ago
1
Change benchmark.py to new schema
#268
dchaley
closed
1 month ago
1
Use gs_fastcopy
#267
dchaley
closed
1 month ago
0
Migrate to gs-fastcopy
#266
dchaley
closed
1 month ago
0
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