Out-of-focus brain image detection in serial tissue sections.
J Neurosci Methods 2020;
345:108852. [PMID:
32771371 DOI:
10.1016/j.jneumeth.2020.108852]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND
A large part of image processing workflow in brain imaging is quality control which is typically done visually. One of the most time consuming steps of the quality control process is classifying an image as in-focus or out-of-focus (OOF).
NEW METHOD
In this paper we introduce an automated way of identifying OOF brain images from serial tissue sections in large datasets (>1.5 PB). The method utilizes steerable filters (STF) to derive a focus value (FV) for each image. The FV combined with an outlier detection that applies a dynamic threshold allows for the focus classification of the images.
RESULTS
The method was tested by comparing the results of our algorithm with a visual inspection of the same images. The results support that the method works extremely well by successfully identifying OOF images within serial tissue sections with a minimal number of false positives.
COMPARISON WITH EXISTING METHODS
Our algorithm was also compared to other methods and metrics and successfully tested in different stacks of images consisting solely of simulated OOF images in order to demonstrate the applicability of the method to other large datasets.
CONCLUSIONS
We have presented a practical method to distinguish OOF images from large datasets that include serial tissue sections that can be included in an automated pre-processing image analysis pipeline.
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