planktoscope/scripts

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Focusing

focus.py nb_step orientation

• nb_step : integer (from 1 to 100000) - number of step to perform by the stage (about 31um/step)
• orientation : string - orientation of the focus either up or down

Example:

python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up

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Pumping

pump.py volume flowrate action

• volume : integer
• flowrate : float
• action : string

Example:

python3.7 $HOME/PlanktonScope/scripts/pump.py 1 10 suck

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Image

image.py in_path sample_project sample_id acq_id volume flowrate

• in_path : string - directory to store acquisitions the path has to end with /
• sample_project : string
• sample_id : string
• acq_id : string
• volume : integer
• flowrate : float

Example:

python3.7 $HOME/PlanktonScope/scripts/image.py $HOME/PlanktonScope/Acquisitions/ tara_pacific station_125 exp_1 24 3.2

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Light

light.py state

• state : string

Example:

python3.7 $HOME/PlanktonScope/scripts/light.py on

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Killing Focus or Pump event

killer.sh event_to_kill.py

• event_to_kill.py : string

Example:

bash $HOME/PlanktonScope/scripts/killer.sh pump.py

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Kill Image

kill_image.sh image.py sample_project sample_id acq_id

• sample_project : string
• sample_id : string
• acq_id : string

Example:

bash $HOME/PlanktonScope/scripts/killer.sh image.py tara_pacific station_125 exp_1