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Helper Page | Jamboree DeepProfiler day

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Michael Bornholdt edited this page Nov 18, 2021 · 9 revisions

Github repos

DeepProfiler repository Cytominer-eval Pycytominer

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Downloading example data

Download this example data! (Ignore Virus error) Unzip file and move to to a convenient location. This is your project folder!

Example self-trained model: Move this to /project/outputs/profile_folder/checkpoints/

Docker

Docker image for today

Pull with docker pull michaelbornholdt/deep_profiler:jamboree

Run with docker run -it --rm -v ~/project_folder:/project_folder michaelbornholdt/deep_profiler:jamboree

Aggregation

Aggregation function

Run Aggregation with code example found in the Wiki

Expected output

Prepare

Reading metadata form /git/tests/example_data//inputs/metadata/index.csv
2021-11-18 15:35:57,197 - INFO - Total plates: 2
/git/tests/example_data//outputs/intensities//Week1_22141/Week1_22141.pkl exists
/git/tests/example_data//outputs/intensities//Week1_22123/Week1_22123.pkl exists
Illumination complete!
Reading metadata form /git/tests/example_data//inputs/metadata/index.csv
2021-11-18 15:35:57,320 - INFO - Total plates: 2
Percentiles for the lower_percentile  >> DNA : 304.0  Tubulin : 736.0  Actin : 368.0  
Percentiles for the upper_percentile  >> DNA : 7728.0  Tubulin : 41888.0  Actin : 20544.0  
Percentiles for the lower_percentile  >> DNA : 288.0  Tubulin : 752.0  Actin : 352.0  
Percentiles for the upper_percentile  >> DNA : 7696.0  Tubulin : 47520.0  Actin : 18768.0  
Progress |##################################################| 100.0% Complete
Progress |##################################################| 100.0% Complete
Compression complete!

Profiling

Running profiling will throw a bunch of warnings - please ignore :)

Extracting output from layer: pool5                                                                                                                   
Week1_22141/B02-s2 (240 cells) : 2.00 secs                                                                                                            
Week1_22141/B03-s2 (56 cells) : 0.27 secs                                                                                                             
Week1_22141/B02-s1 (276 cells) : 3.82 secs                                                                                                            
Week1_22141/B04-s1 (90 cells) : 0.45 secs                                                                                                             
Week1_22141/B03-s1 (103 cells) : 0.42 secs                                                                                                            
Week1_22141/B04-s2 (104 cells) : 0.44 secs                                                                                                            
Week1_22123/B03-s1 (112 cells) : 0.48 secs                                                                                                            
Week1_22123/B04-s1 (89 cells) : 0.36 secs                                                                                                             
Week1_22123/B03-s2 (28 cells) : 0.13 secs                                                                                                             
Week1_22123/B04-s2 (79 cells) : 0.34 secs                                                                                                             
Week1_22123/B02-s2 (149 cells) : 0.69 secs                                                                                                            
Week1_22123/B02-s1 (206 cells) : 1.04 secs                                                                                                            
Profiling: done

Aggregation

Aggregating features in /git/tests/example_data/outputs/pre/features
Week1_22141/B02
Week1_22141/B03
Week1_22141/B04
Week1_22123/B03
Week1_22123/B04
Week1_22123/B02

Don't cheat

Compression results

Profile results

!

Heading

  1. download example data to /jamboree/
  2. unzip example_data.zip
  3. docker run -it --rm -v ~/jamboree:/jamboree michaelbornholdt/deep_profiler:jamboree
  4. check that the mount worked: ls /jamboree/example_data/ should give inputs and outputs
  5. python3 deepprofiler --root=/jamboree/example_data/ --config=config.json prepare
  6. in /jamboree/example_data/inputs/config/config.json change the profile: checkpoint to "None"
  7. python3 deepprofiler --root=/jamboree/example_data/ --config=config.json profile
  8. create aggregate.py in /example_data/ with code above and run it.
  9. DONE! :)
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