FAIM Wako SearchFirst

Table of Contents

• Installation
• License

Installation

pip install faim-wako-searchfirst

Usage

Configuration is managed in a config.yml file:

# Required
file_selection:  # criteria for file selection in case of multiple channels/slices per position
    channel: C01
process:  # choose method how to segment, filter, and sample the objects
    segment: threshold  # choices: threshold, cellpose
    filter: [bounding_box, area, solidity, intensity]
    sample: centers  # choices: centers, grid_overlap, dense_grid

# Each subsequent section provides arguments to one of the methods defined in 'process'
threshold:
    threshold: 128
    include_holes: yes
    gaussian_sigma: 2.0 # optional 
bounding_box:
    min_x: 64
    min_y: 0
    max_x: 256
    max_y: 190
area:
    min_area: 100
    max_area: 10000
solidity:
    min_solidity: 0.9
    max_solidity: 1.0
intensity:
    target_channel: C03
    min_intensity: 128

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

import typer
from faim_wako_searchfirst.main 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.