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dchaley
/
deepcell-imaging
Tools & guidance to scale DeepCell imaging on Google Cloud Batch
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Remote output squeeze option
#265
dchaley
closed
3 days ago
0
Use gcloud_storage_utils for writing TIFF to GCP
#264
dchaley
closed
3 days ago
0
Output predictions tiff in benchmark script
#263
dchaley
closed
3 days ago
1
Try keras save format for faster model load
#262
dchaley
opened
1 week ago
0
Push builds to GCP Artifact Registry and Docker Hub
#261
dchaley
closed
1 week ago
1
Switch from building on GitHub Actions to Cloud Build
#260
dchaley
closed
1 week ago
0
Github action: build container for branch main
#259
dchaley
closed
1 week ago
0
Skip gather-benchmark when table is empty
#258
dchaley
closed
1 week ago
0
Add bigquery table name param. Empty to disable.
#257
dchaley
closed
1 week ago
0
Convert gcloud storage fetch_file to idiomatic reader
#256
dchaley
closed
1 week ago
0
Improve gcloud storage writes
#255
dchaley
closed
1 week ago
0
Automate container build
#254
dchaley
closed
1 week ago
3
Support tiff visualization output
#253
dchaley
opened
1 week ago
10
Use pigz and add gcloud storage to container
#252
dchaley
closed
1 week ago
0
Parameterize run-job model_path
#251
dchaley
closed
1 week ago
0
Parameterize model_path on run-job for Batch
#250
dchaley
closed
1 week ago
0
Use gcloud storage cp instead of Python API
#249
dchaley
closed
1 week ago
0
Speed up cloud storage interaction
#248
dchaley
closed
1 week ago
4
Fetch input image size from remote file (don't hardcode)
#247
dchaley
closed
2 weeks ago
0
Verify Batch network interface in allocation policy
#246
dchaley
closed
6 days ago
2
Add mechanism to turn off BigQuery
#245
dchaley
closed
1 week ago
1
Add benchmark gather script + missing benchmark fields
#244
dchaley
closed
2 weeks ago
0
WIP scripts to run on GCE directly. NOTE: UNTESTED!
#243
dchaley
closed
2 weeks ago
0
Run container by hand on GCE instance
#242
dchaley
closed
2 weeks ago
4
Update the 'About' description
#241
langitlynn
closed
1 day ago
1
Remove hard-coded 512x512 size for postprocess step
#240
dchaley
closed
2 weeks ago
3
Add benchmarking output to pre/infer/post steps
#239
dchaley
closed
3 weeks ago
0
Move benchmark data to bucket + add final step to record it
#238
dchaley
closed
2 weeks ago
4
Small fixes
#237
dchaley
closed
3 weeks ago
0
Add entrypoint scripts + pyproject.toml + install self in container
#236
dchaley
closed
3 weeks ago
0
Allow deepcell_imaging module to run in "development mode" in the venv
#235
dchaley
closed
3 weeks ago
1
Define the command-line interface for each step
#234
dchaley
closed
3 weeks ago
2
Extract mesmer app predict phases
#233
dchaley
closed
4 weeks ago
0
Figure out model_zoo fix [arm64]
#232
dchaley
opened
4 weeks ago
0
Add dependencies we need installed
#231
dchaley
closed
1 month ago
0
Update README with git lfs instructions
#230
dchaley
opened
1 month ago
0
Requirements and instructions for running on Mac silicon
#229
dchaley
closed
1 month ago
0
Use new base: 11.8.0-cudnn8-runtime-ubuntu22.04
#228
dchaley
closed
1 month ago
0
Switch container base to rebuilt 2.8.4-gpu image
#227
dchaley
closed
1 month ago
0
Investigate rebuilding TF2.8 container
#226
dchaley
closed
1 month ago
3
Investigate cloud build caching
#225
dchaley
opened
1 month ago
1
Parameterize the BQ table target
#224
dchaley
closed
1 month ago
0
Add script to submit a batch job
#223
dchaley
closed
1 month ago
0
Create entry points for preprocess, infer, and postprocess
#222
dchaley
closed
3 weeks ago
2
Add script to build new image
#221
dchaley
closed
1 month ago
0
Some logs in Batch show up as errors but aren't
#220
dchaley
opened
1 month ago
2
Generate job directory & job id for benchmark automatically
#219
dchaley
closed
1 month ago
0
Parameterize DeepCell benchmarking BigQuery upload target
#218
dchaley
closed
1 month ago
0
No feedback for job completion
#217
dchaley
opened
1 month ago
0
Add readme to run jobs & sample batch json to new parameters
#216
dchaley
closed
1 month ago
0
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