Software tools and platforms in Digital Pathology: a review for clinicians and computer scientists

Guerrero, Rodrigo Escobar Díaz; Carvalho, Lina; Bocklitz, Thomas; Popp, Juergen; Oliveira, José Luís

doi:10.1016/j.jpi.2022.100103

Cited by 15 publications

(9 citation statements)

References 57 publications

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“… 40 , 41 In contrast, open-source software, including CellProfiler, allows image analysis methods and codes not only to be accessible to investigators but also to be interrogated, extended, enhanced, and shared by a wider community, which can solve the majority of the challenges around data management, visualization, and interactivity while permitting others to add new algorithms and functionality for specific tasks. 39 , 42 , 43 CellProfiler is an image analysis software released in 2005 and has since undergone a series of improvements to become one of the most widely used forms of software for pathomics analyses due to its versatility, continuous improvements, and ease of use. 24 , 43 Although some useful features might be ignored by using the inherent software extraction method of CellProfiler, there is no perfect software or method providing features that support all studies; thus, a more suitable software or method can be selected for individual research needs.…”

Section: Discussionmentioning

confidence: 99%

“… 39 , 42 , 43 CellProfiler is an image analysis software released in 2005 and has since undergone a series of improvements to become one of the most widely used forms of software for pathomics analyses due to its versatility, continuous improvements, and ease of use. 24 , 43 Although some useful features might be ignored by using the inherent software extraction method of CellProfiler, there is no perfect software or method providing features that support all studies; thus, a more suitable software or method can be selected for individual research needs. 43 …”

Section: Discussionmentioning

confidence: 99%

“… 24 , 43 Although some useful features might be ignored by using the inherent software extraction method of CellProfiler, there is no perfect software or method providing features that support all studies; thus, a more suitable software or method can be selected for individual research needs. 43 …”

Section: Discussionmentioning

confidence: 99%

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et al. 2023

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Predicting peritoneal recurrence in gastric cancer with serosal invasion using a pathomics nomogram

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“…Therefore, pathologists require efficient annotation tools (preferably open-source) that easily enable them to label patterns in WSIs . Hopefully, such software are available (see [184] for a complete review):…”

Section: A Lack In Quality Of Labelsmentioning

confidence: 99%

Whole Slide Image Quality in Digital Pathology: Review and Perspectives

Brixtel¹,

Bougleux

Lézoray

et al. 2022

IEEE Access

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With the advent of whole slide image (WSI) scanners, pathology is undergoing a digital revolution. Simultaneously, with the development of image analysis algorithms based on artificial intelligence tools, the application of computerized WSI analysis can now be expected. However, transferring such tools into clinical practice is very challenging as they must deal with many artifacts that can occur during sample preparation and digitization. Therefore, the quality of WSIs is of prime importance, and we propose a review of the state-of-the-art of computational approaches for quality control. In particular, we focus on WSI quality issues related to the presence of sample preparation artifacts, compression artifacts, color variations, and out-of-focus areas. An analysis of the monthly WSI clinical routine in a cytological laboratory confirms the importance of implementing quality control measures. Given this observation, we draw perspectives on how a computational quality process can be included in a computational pathology diagnosis pipeline.

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“…Numerous proprietary digital IA software suites are commercially available for a variety of applications 7 . Drawbacks to these solutions include cost and potential lack of cross-compatibility and customizability, which may render them prohibitive for smaller practices with fewer resources.…”

mentioning

confidence: 99%

Implementation of Digital Image Analysis in Assessment of Ki67 Index in Breast Cancer

Vanderschelden,

Jerome,

Gonzalez

et al. 2023

Applied Immunohistochemistry &Amp; Molecular Morphology

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The clinical utility of the proliferation marker Ki67 in breast cancer treatment and prognosis is an active area of research. Studies have suggested that differences in pre-analytic and analytic factors contribute to low analytical validity of the assay, with scoring methods accounting for a large proportion of this variability. Use of standard scoring methods is limited, in part due to the time intensive nature of such reporting protocols. Therefore, use of digital image analysis tools may help to both standardize reporting and improve workflow. In this study, digital image analysis was utilized to quantify Ki67 indices in 280 breast biopsy and resection specimens during routine clinical practice. The supervised Ki67 indices were then assessed for agreement with a manual count of 500 tumor cells. Agreement was excellent, with an intraclass correlation coefficient of 0.96 for the pathologist-supervised analysis. This study illustrates an example of a rapid, accurate workflow for implementation of digital image analysis in Ki67 scoring in breast cancer.

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Software tools and platforms in Digital Pathology: a review for clinicians and computer scientists

Cited by 15 publications

References 57 publications

Predicting peritoneal recurrence in gastric cancer with serosal invasion using a pathomics nomogram

Predicting peritoneal recurrence in gastric cancer with serosal invasion using a pathomics nomogram

Whole Slide Image Quality in Digital Pathology: Review and Perspectives

Implementation of Digital Image Analysis in Assessment of Ki67 Index in Breast Cancer

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