![]() This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: The authors confirm that, for approved reasons, some access restrictions apply to the data underlying the findings. Received: JAccepted: SeptemPublished: November 5, 2014Ĭopyright: © 2014 Nelissen et al. PLoS ONE 9(11):Įditor: Anna Sapino, University of Torino, Italy In conclusion, slideToolkit provides a free, powerful and versatile collection of tools for automated feature analysis of whole slide images to create reproducible and meaningful phenotypic data sets.Ĭitation: Nelissen BGL, van Herwaarden JA, Moll FL, van Diest PJ, Pasterkamp G (2014) SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images. Using this method, two consecutive measurements of 303 slides showed an intraclass correlation of 0.99. In the fourth step (analysis), tissue is analyzed and results are stored in a data set. The third step (tiles), creates multiple manageable tiles to count. ![]() In the second step (preparation), files are organized. In the first step (acquisition), whole slide images are collected and converted to TIFF files. Our workflow consists of four consecutive steps. We here illustrate the power of slideToolkit by a repeated measurement of 303 digital slides containing CD3 stained (DAB) abdominal aortic aneurysm tissue from a tissue biobank. The slideToolkit has been developed for modern personal computers and high-performance clusters (HPCs) and is available as an open-source project on. In order to comply with this need, we developed the slideToolkit as a fast method to handle large quantities of low contrast whole slides images using advanced cell detecting algorithms. ![]() Relatively few free toolkits are, however, available for fully digitized microscopic slides, usually known as whole slides images. Therefore, within our own biobank, computerized quantification of digitized histological slides is often preferred as a more precise and reproducible, and sometimes more sensitive approach. Nonetheless, purely visual assessment of histological slides is time-consuming and liable to sampling variation and optical illusions and thereby observer variation, and external validation may be cumbersome. Detailed analysis of histology is a powerful way of phenotyping human tissues. The demand for accurate and reproducible phenotyping of a disease trait increases with the rising number of biobanks and genome wide association studies.
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