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Out-of-focus brain image detection in serial tissue sections.

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Title: Out-of-focus brain image detection in serial tissue sections.
Authors: Pollatou, Angeliki1,2 (AUTHOR) af3215@cumc.columbia.edu, Ferrante, Daniel D.2 (AUTHOR)
Source: Journal of Neuroscience Methods. Nov2020, Vol. 345, pN.PAG-N.PAG. 1p.
Subjects: Brain imaging, Inspection & review, Outlier detection, Image analysis, Quality control
Abstract: • A new method of identifying out-of-focus images in serial tissue sections is proposed. • The method combines steerable filters and outliers detection to locate out-of-focus images. • Comparisons with visual inspections show the method has high recall and precision. • The method outperforms others and can be used for a variety of datasets. • The method can be automated and implemented in a pipeline. 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). 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. 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. 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. 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. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Neuroscience Methods is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
An: 145678948
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
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  Data: Out-of-focus brain image detection in serial tissue sections.
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  Data: <searchLink fieldCode="AR" term="%22Pollatou%2C+Angeliki%22">Pollatou, Angeliki</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<i> af3215@cumc.columbia.edu</i><br /><searchLink fieldCode="AR" term="%22Ferrante%2C+Daniel+D%2E%22">Ferrante, Daniel D.</searchLink><relatesTo>2</relatesTo> (AUTHOR)
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  Data: <searchLink fieldCode="DE" term="%22Brain+imaging%22">Brain imaging</searchLink><br /><searchLink fieldCode="DE" term="%22Inspection+%26+review%22">Inspection & review</searchLink><br /><searchLink fieldCode="DE" term="%22Outlier+detection%22">Outlier detection</searchLink><br /><searchLink fieldCode="DE" term="%22Image+analysis%22">Image analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Quality+control%22">Quality control</searchLink>
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  Label: Abstract
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  Data: • A new method of identifying out-of-focus images in serial tissue sections is proposed. • The method combines steerable filters and outliers detection to locate out-of-focus images. • Comparisons with visual inspections show the method has high recall and precision. • The method outperforms others and can be used for a variety of datasets. • The method can be automated and implemented in a pipeline. 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). 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. 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. 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. 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. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
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  Data: <i>Copyright of Journal of Neuroscience Methods is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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RecordInfo BibRecord:
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      – Type: doi
        Value: 10.1016/j.jneumeth.2020.108852
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      – Code: eng
        Text: English
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        PageCount: 1
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      – SubjectFull: Brain imaging
        Type: general
      – SubjectFull: Inspection & review
        Type: general
      – SubjectFull: Outlier detection
        Type: general
      – SubjectFull: Image analysis
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      – SubjectFull: Quality control
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      – TitleFull: Out-of-focus brain image detection in serial tissue sections.
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            NameFull: Pollatou, Angeliki
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            NameFull: Ferrante, Daniel D.
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              M: 11
              Text: Nov2020
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              Y: 2020
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              Value: 345
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