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Project description
FAIM Wako SearchFirst
Table of Contents
Installation
pip install faim-wako-searchfirst
Usage
Configuration is managed in a config.yml
file:
# Required
# criteria for file selection in case of multiple channels/slices per position
file_selection:
channel: C01
# choose method how to segment, filter, and sample the objects
process:
# segment methods: threshold, cellpose
segment: threshold
# filter methods: bounding_box, area, solidity, intensity
filter: [bounding_box, area, solidity, feature, dilate, intensity]
# sample methods: centers, grid_overlap, dense_grid,
# object_centered_grid, region_centered_grid
sample: centers
# Each section below provides arguments to one of the methods set in 'process'.
# Config sections for methods not selected above will be ignored.
# segment
threshold:
threshold: 128
include_holes: true
gaussian_sigma: 0.0 # default: 0.0
# filter
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
feature:
feature: eccentricity
min_value: 0.0
max_value: 0.99
dilate:
pixel_distance: 1.0
intensity:
target_channel: C03
min_intensity: 128
# sample
dense_grid:
binning_factor: 50 # default: 50
grid_overlap:
mag_first_pass: 4
mag_second_pass: 60
overlap_ratio: 0.05 # default: 0
object_centered_grid:
mag_first_pass: 4
mag_second_pass: 60
overlap_ratio: 0.05 # default: 0
region_centered_grid:
mag_first_pass: 4
mag_second_pass: 60
overlap_ratio: 0.05 # default: 0
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.
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