Auto-threshold Channel Intensity — autothreshold • SpatialMap

Given an image, and two parameters (analogous to min and max), returns a new max and min value for the image, between which the image's intensity values can be re-scaled to highlight it's true dynamic range.

Usage

autothreshold(image, auto.threshold = 5000, max.limit = 10)

Arguments

image: An image object
auto.threshold: High pass threshold. The total number of pixels is divided by auto.threshold; a bin of values must contain this number of pixels to be included in the new range
max.limit: Low pass threshold. The total number of pixels is divided by max.limit; a bin of values must contain this number of pixels to be included in the new range

from https://gitlab.com/enable-medicine/cloud-image-viewer/-/blob/master/serverless/batch/bf_auto_threshold.py

1/AUTO_THRESHOLD is set as the minimum proportion of threshold bin to consider AUTO_THRESHOLD = 5000 1/MAX_LIMIT is set as the maximum proportion of threshold bin to consider MAX_LIMIT = 10