DOI: 10.5061/dryad.v9s4mw749
title: Data from: Reinterpretation of prostate cancer pathology by Appl1, Sortilin and Syndecan-1 biomarkers

description: The diagnosis of prostate cancer using histopathology is reliant on the
 accurate interpretation of stained or labelled tissue sections. Current
 standards rely on assessment following Haematoxylin and Eosin
 (H&E) staining, which is often difficult to interpret and
 introduces inter-observer variability. Here, we present a digital
 pathology atlas for prostate cancer tissue, using micrographs of both
 H&E and our novel set of three biomarkers as an interactive tool,
 where clinicians and scientists can explore high resolution histopathology
 from various case studies. The digital pathology prostate cancer atlas
 when used in conjunction with the biomarkers, will greatly assist
 pathologists to accurately grade prostate cancer tissue samples. This
 repository also contains the original image dataset used to generate the
 case studies for the digital pathology atlas. The data consist of a benign
 case and cases of ISUP grades from 1 to 5, where initial grading was
 performed on the hematoxylin and eosin (H&E) stained tissue
 section, along with three serial sections from the same tissue block,
 labeled with our biomarker panel - Appl1, Sortilin, and Syndecan-1. This
 biomarker panel was then used to assist the initial H&E grading,
 providing a more accurate diagnosis and prognosis from the retrospective
 patient dataset.
description: All images were acquired using a Carl ZEISS AxioScan.Z1
 microscope, with a Planapochromat 40x/0.95 objective. Images were
 orginially stored in the native Carl ZEISS Image format (*.CZI), and then
 converted to BigTIFF format using Carl ZEISS Zen Blue Software (version
 3.8). Lossless compression was also used to minimise file sizes, while
 retaining image quality. All images can be  using freely available imaging
 software, such as ImageJ or FiJi.
description: # Reinterpretation of prostate cancer pathology by Appl1, Sortilin and
 Syndecan-1 biomarkers
 [https://doi.org/10.5061/dryad.v9s4mw749](https://doi.org/10.5061/dryad.v9s4mw749) We present a digital pathology atlas for prostate cancer tissue, using micrographs of both H&E (hematoxylin and eosin) and our novel set of three biomarkers as an interactive tool, where clinicians and scientists can explore high resolution histopathology from various case studies. The digital pathology prostate cancer atlas when used in conjunction with the biomarkers, will greatly assist pathologists to accurately grade prostate cancer tissue samples. The full set of digital micrographs are also accessible in this repository, along with the grading and patient outcome data. ## Description of the data and file structure The digital pathology atlas for prostate cancer is a fully interactive portable document format (PDF) file, where users can easily explore high resolution histopathology from various case studies. A usage video is also provided, helping to guide users in how to use the atlas. The micrographs of the case studies are individually labelled based on their grade group and stain or biomarker label. All micrographs were originally acquired using the Carl ZEISS Image format (CZI), using a Carl ZEISS AxioScan.Z1 microscope using a Planachromat 40x/0.95 objective. The micrographs were then converted to BigTIFF format for open access. A comma spaced value (CSV) file is also available, showing initial grading by H&E, and the improved grading using the biomarker panel assisted grading. ### The digital pathology atlas * The_Digital_Pathology_Prostate_Cancer_Atlas.pdf * Atlas_Usage_Video.mp4 * The_Digital_Pathology_Prostate_Cancer_Atlas_images_only.zip This interactive document allows pathologists to view example prostate cancer tissue sections, ranging from benign to ISUP grades 1 through 5 (International Society of Urological Pathology). The sections presented are stained with H&E and labeled with our biomarkers: Appl1, Sortilin, and Syndecan-1. An example usage video is also available, demonstrating the functionality of the atlas. Additionally, an image only version of this document is also available as a series of JPEG images (The_Digital_Pathology_Prostate_Cancer_Atlas_images_only.zip). ### Digital micrographs Digital micrographs of complete prostate tissue sections are available in BigTIFF format. These include H&E stained sections and sections labeled with Appl1, Sortilin, and Syndecan-1 for benign tissue and ISUP grades 1 through 5 prostate cancer tissue. Filenames are labeled according to their grading and respective stain or label (e.g., ISUP2_Sortilin.tif indicates a section graded as ISUP 2 and labeled with Sortilin). *Benign Case* * Benign_Appl1.tif * Benign_HE.tif  * Benign_Sortilin.tif * Benign_Syndecan-1.tif *ISUP 1 Case* * ISUP1_Appl1.tif * ISUP1_HE.tif * ISUP1_Sortilin.tif * ISUP1_Syndecan-1.tif *ISUP 2 Case* * ISUP2_Appl1.tif * ISUP2_HE.tif * ISUP2_Sortilin.tif * ISUP2_Syndecan-1.tif *ISUP 3 Case* * ISUP3_Appl1.tif * ISUP3_HE.tif * ISUP3_Sortilin.tif * ISUP3_Syndecan-1.tif *ISUP 4 Case* * ISUP4_Appl1.tif * ISUP4_HE.tif * ISUP4_Sortilin.tif * ISUP4_Syndecan-1.tif *ISUP 5 Case* * ISUP5_Appl1.tif * ISUP5_HE.tif * ISUP5_Sortilin.tif * ISUP5_Syndecan-1.tif A CSV file containing the original grading by H&E and the biomarker assisted grade is also available. * Case_Study_Grading.csv ## Code/Software The atlas is best viewed using Adobe Acrobat, either Acrobat Reader or Acrobat Professional can be used to enable full compatibility and interactivity of the atlas, while the atlas can be viewed within an internet browser, the interactive functions maybe limited. Micrographs can be opened using freely available imaging software, such as ImageJ or FiJi.