config_LENS_M3_t6.yaml 1.6 KB

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  1. # Config file for Stage 1 - Data Entry
  2. # Name of stage, must be identical with folder name
  3. STAGE_NAME: 'stage01_data_entry'
  4. # The profile name is the key for this parameter configuration. Results are stored in output_path/<PROFILE>/ (output_path is defined in settings.py)
  5. PROFILE: 'LENS_M3_t6'
  6. # Name of stage output file.
  7. STAGE_OUTPUT: "data.nix"
  8. # File format in which all intermediate neo objects are stored
  9. NEO_FORMAT: 'nix'
  10. # If True (default), the output file of a stage is created as symbolic link
  11. # to the last block output. If False, a duplicate is created (e.g. for cloud
  12. # application, where sym-links are not supported).
  13. USE_LINK_AS_STAGE_OUTPUT: True
  14. # Datasets which should be processed with identical settings.
  15. # To set as key-value pairs
  16. # Name_of_dataset: /path/to/data/files/
  17. DATA_SETS:
  18. LENS_GCMaP6f_mouse3_t6: '/projects/wavescalephant/Data/LENS/Slow-wave 1/170111/mouse 3/deep/t6'
  19. CURATION_SCRIPT: 'curate_LENS_data.py'
  20. # pixel size
  21. SPATIAL_SCALE: 0.05 # mm
  22. SAMPLING_RATE: 25 # Hz
  23. # time slice in s
  24. # if None, the entire recording is used
  25. T_START: None
  26. T_STOP: None
  27. # recommend top: ventral
  28. ORIENTATION_TOP: 'ventral'
  29. # recommended right: 'lateral' for right hemisphere, 'medial' for left hemisphere
  30. ORIENTATION_RIGHT: 'lateral'
  31. # Metadata
  32. ANNOTATIONS:
  33. technique: calcium imaging
  34. doi: 10.25493/QFZK-FXS
  35. anesthetic: ketamine-xylazine
  36. concentration: 100 & 10 mg/kg
  37. model_type: 'WT'
  38. ARRAY_ANNOTATIONS: 'None'
  39. KWARGS: 'None'
  40. # Plot settings
  41. PLOT_TSTART: 0 # in s
  42. PLOT_TSTOP: 10 # in s
  43. PLOT_CHANNELS: [4040, 5050, 6060] # int, list of ints, or 'None' (default) -> picks channel by random
  44. PLOT_FORMAT: 'png'