production

Production

Usage

Add configuration for the production, gain, leica and rename plugin, in the camacq configuration file. See the config_templates directory for example configuration.

production:
  ...

gain:
  ...

rename_image:

leica:
  ...

Then start camacq.

camacq

To allow the user to set up the sample state before starting an experiment, camacq can load the sample state from a file. In the production configuration section there is an option to specify a path to a csv file.

production:
  sample_state_file: '/sample_state.csv'

Each row in the csv file should represent at least one state of a sample container, ie well, field, channel or z_slice. A plate name must also be included. The csv file should have a header. The first column should have the name of the most low level container to create. Eg a field must be part of a well which must be part of a plate, so field is the most low level container of those containers. See below.

name,plate_name,well_x,well_y,channel_id
channel,00,1,1,0

This example will set a plate '00', a well (1, 1), and a channel with channel id 0.

name,plate_name,well_x,well_y,field_x,field_y
field,00,1,1,1,1

This example will create a plate '00' a well (1, 1) and a field (1, 1) in the sample state.