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- # Config file for Stage 1 - Data Entry
- # Name of stage, must be identical with folder name
- STAGE_NAME: 'stage01_data_entry'
- # The profile name is the key for this parameter configuration. Results are stored in output_path/<PROFILE>/ (output_path is defined in settings.py)
- PROFILE: 'LENS_ISO190109_t2'
- # Name of stage output file.
- STAGE_OUTPUT: "data.nix"
- # File format in which all intermediate neo objects are stored
- NEO_FORMAT: 'nix'
- # If True (default), the output file of a stage is created as symbolic link
- # to the last block output. If False, a duplicate is created (e.g. for cloud
- # application, where sym-links are not supported).
- USE_LINK_AS_STAGE_OUTPUT: True
- # Datasets which should be processed with identical settings.
- # To set as key-value pairs
- # Name_of_dataset: /path/to/data/files/
- DATA_SETS:
- LENS_ISO190109_t2: '/projects/wavescalephant/Data/LENS_ISO/190109/t2'
- CURATION_SCRIPT: 'curate_LENS_data.py'
- # pixel size
- SPATIAL_SCALE: 0.05 # mm
- SAMPLING_RATE: 25 # Hz
- # time slice in s
- # if None, the entire recording is used
- T_START: None
- T_STOP: 75
- # recommend top: ventral
- ORIENTATION_TOP: 'ventral'
- # recommended right: 'lateral' for right hemisphere, 'medial' for left hemisphere
- ORIENTATION_RIGHT: 'lateral'
- # Metadata
- ANNOTATIONS:
- technique: calcium imaging
- doi: 10.25493/XJR8-QCA
- anesthetic: isoflurane
- concentration: 1-2%
- model_type: 'WT'
- ARRAY_ANNOTATIONS: 'None'
- KWARGS: 'None'
- # Plot settings
- PLOT_TSTART: 0 # in s
- PLOT_TSTOP: 10 # in s
- PLOT_CHANNELS: [4040, 5050, 6060] # int, list of ints, or 'None' (default) -> picks channel by random
- PLOT_FORMAT: 'png'
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