Example Parsing Notebook to rename phenix experiments

[2]:

import os
os.environ['JAVA_HOME'] = "/Users/sophia/mambaforge/envs/scPortrait/lib/jvm"
from scportrait.tools.parse import PhenixParser

[3]:

input_dir = "path/to/phenix/experiment" #do not need to go to the image directory, the main directory is sufficient

[3]:

print("Beginning Parsing")
parser = PhenixParser(input_dir)
parser.parse()
print("Parsing completed.")

Beginning Parsing
Experiment contains the following image channels:
  id         label
0  1      Alexa647
1  2       mCherry
2  3  HOECHST33342
3  4   Brightfield

Channel Lookup table saved to file at /fs/pool/pool-mann-projects/Thierry_N/ForPeople/SophiaMaedler/A375wm40_cc14_ctrl1_tmt1o3_20240525/channel_lookuptable.csv

Starting copy process...

Copying files: 100%|██████████| 35392/35392 [00:03<00:00, 9012.68it/s]

Copy process completed.
Checking for missing images...
No missing tiles found.
Metadata used to parse images saved to file /fs/pool/pool-mann-projects/Thierry_N/ForPeople/SophiaMaedler/A375wm40_cc14_ctrl1_tmt1o3_20240525/metadata_image_parsing.csv
Parsing completed.