CellProfiler/CellProfiler — Issue #153: JIRA [IMG-1025] Implement illumination correction using foreground segmentation
Author: thouis
Created: 2011-11-23 20:50:24+00:00
State: open
Labels: future

first identify foreground objects using methods insensitive to illumination variation (what would those be exactly??)
use mean intensities of objects and their locations across images to create the function
use trimmed mean filtering as well as image by image rejection based on QC metrics to handle artificially bright outliers (debris)

Original reporter: klmadden
Jira link: https://jira.broadinstitute.org/browse/IMG-1025
Fix version: Future
Assignee: leek

**Comment from anne on Mon, 25 Apr 2011 17:40:54 -0400:**
From the CP SW grant:
"We will implement new methods to handle well edges and nonlinear responses by first identifying
foreground objects using methods that are insensitive to illumination variation. The mean intensities of
these objects and their locations can be combined to find the illumination bias across a set of images,
emphasizing accuracy for the foreground objects, but with accuracy elsewhere that is sufficient for
segmentation purposes84. To handle outliers that contain artifactually bright signals, we will use robust
estimation85 (e.g., trimmed mean filtering86), as well as image-by-image rejection based on quality-control
metrics. These methods will be tested and provided as additional options in CellProfiler, along with
guidance to the user as to which methods are appropriate under which conditions."