FAIM Wako SearchFirst

Table of Contents

• Installation
• License

Installation

pip install faim-wako-searchfirst

Usage

Configuration is managed in a config.yml file:

file_selection:
    channel: C01
segmentation:
    threshold: 128
    include_holes: yes
    min_size: 10
    max_size: 99999999999
    min_eccentricity: 0.0
    max_eccentricity: 0.4
bounding_box:
    min_x: 0
    min_y: 0
    max_x: 256
    max_y: 256
additional_analysis:
    enabled: yes
    target_channel: C03
    min_intensity: 128
output:
    type: grid
grid_sampling:
    mag_first_pass: 4
    mag_second_pass: 40
    overlap_percent: 0
    offset_grid_origin_percent: 50

The Python script called by Wako Automation Software needs to accept the acquisition folder folder_path as only parameter:

import typer as typer
from faim_wako_searchfirst.segment import run

def main(folder_path: str):
    run(folder=folder_path, configfile="config.yml")

if __name__ == "__main__":
    typer.run(main)

License

faim-wako-searchfirst is distributed under the terms of the MIT license.