Digitization of Pathology Labs: A Review of Lessons Learned

Pathology laboratories are increasingly using digital workflows. This has the potential of increasing lab efficiency, but the digitization process also involves major challenges. Several reports have been published describing the individual experiences of specific laboratories with the digitization process. However, a comprehensive overview of the lessons learned is still lacking. We provide an overview of the lessons learned for different aspects of the digitization process, including digital case management, digital slide reading, and computer-aided slide reading. We also cover metrics used for monitoring performance and pitfalls and corresponding values observed in practice. The overview is intended to help pathologists, IT decision-makers, and administrators to benefit from the experiences of others and to implement the digitization process in an optimal way to make their own laboratory future-proof.Comment: 22 pages, 1 figur

Development Of An Android Based Interactive Guide For The Berliner Medizinhistorisches Museum Der Charité

Introduction/ Background Pathology is the science of diseases that ranges from macroscopic to histologic, and of course molecular changes. To offer a holistic education we wanted to involve portable electronic devices to combine information on diseases with microscopic changes and formalin fixed organs (macroscopic preparation). Aims At the time of compilation of this application there was no alternative, useful solution that offers the possibility of extensions towards virtual microscopy. Moreover, other solutions always use fixed databases or do not provide tools for content updates. Hence, it was required to create an appropriate system. Additional aimed feature are high performance, data-caching and the opinion to use the app in offline mode without a network connection. By the reason of the large amount of smartphone and tablet computer that runs the Android operating system and cheaper devices this platform was used. Methods We combined our virtual microscope „AndroScope“ [1] with a new developed user-interface of the „Berliner Medizinhistorisches Museum“(BMM) for android based mobile devices such as smartphone and tablet computer. As content we used images of the exhibition samples, information on the corresponding organ and disease, as well as the epidemiology data and whole slide images for visualization of histological changes. Linkage of digital content and samples is realized using QR-codes to assure valid and user-friendly recognition. We have also evaluated other technologies such as NFC, Bluetooth, WiFi or GPS to ensure that the QR-Code solution is the best opinion [2]. The application offers an online mode with full functionality and an offline mode with limited access to images as well as to the virtual microscope. The application main database is stored local on the android device and online update capabilities were added. Results The “BMM Guide” is available for all visitors of the museum on lendable devices or for students (professional audience) using their personal devices and installing the application manually via the web-access eduroam. The guide is connected to the internet. It is designed to easily expand, update or transfer the content catalogue data. At the moment there is a connection between the exhibit and text-, image-, video- or virtual microscope content via QR-Code. The offline mode is limited to the connection between text content and the exhibit. We also implemented a multi-language support for English and German. The application has information like room plans, opening times and latest news of the museum. The museum guide is an easy handable, selfexplaining blended learning tool that can be embedded in the general education. .This guide for the exhibitions of the Berliner Medizinhistorisches Museum opens a new branch for self-study of students. Nevertheless he still has a potential to be integrated in curricular lectures in the future

Block-Centric Visualization Of Histological Whole Slide Images With Application To Revealing Growth-Patterns Of Early Colorectal Adenomas And Aberrant Crypt Foci

Introduction/ Background Comfortable navigation through diagnostic images is a prospective challenge for the acceptance of virtual microscopy applications in routine pathology [1],[2]. Tracing different regions of interest through multiple sections on one or several slides is a typical task in diagnostic slide examination. This laborious and time-consuming co-localization is currently executed by pathologists. Retaining the relative positions of tissue structures while alternating between multiple slides is still not feasible in a satisfactory manner in conventional nor virtual microscopy. Aims To address this issue we present a more comfortable and intuitive method to read slides using computer-assisted navigation. Furthermore, we demonstrate the strengths of our method by applying it to large series of serial colorectal tissue sections, creating new kinds of visualizations of different adenomatous mucosal architectures in human tissue, while looking for human correlates of lesions recently described in mice [3]. Methods Histological images contain multiple distortions from different sources in the laboratory and digitalization process. An interconnection model was created to describe distortions by several layers, providing a normalized tissue representation. Layers were associated with specific distortions with each layer serving as a new level of abstraction. The first layers enabled a coarse alignment of tissue sections. Further alignment is achieved by piecewise, multi-resolution, SIFT-based [4] correspondence extraction and refinement. Inside the convex hull of all fiducial points local affine transformations were applied whereas a global affine transformation was used on the outside. Animated stacks were generated for regions of interest using local rigid transformations to preserve exact morphological coherences. For subsequent creation of 3D models, the relevant histological objects within these images were annotated by pathologists, partly using computer assisted segmentation based on active contours [5]. These annotations were used subsequently to create simplified 3D models by applying VTK [6].  Results The presented methods provide an efficient means to retrieve correspondences and additional spatial information from serial sections of histological slides. They also show good applicability for specimen from different origin. Alignment methods can be applied to generate block-centric visualizations such as parallel and transparent viewing of multiple stains. Moreover, the generated stack videos and 3D models demonstrate the very good accuracy of section alignment even in large series. The visualizations enable pathologists and researchers to grasp the 3D structural relationships in the tissue at a glance, providing an excellent tool to communicate more complex histomorphological findings. Interestingly, we see two kinds of tubular adenomas, which could imply multiple ways to tubular adenoma formation in FAP-patients, possibly akin to the recent observations in mice [3]

Best Practice Recommendations for the Implementation of a Digital Pathology Workflow in the Anatomic Pathology Laboratory by the European Society of Digital and Integrative Pathology (ESDIP)

The interest in implementing digital pathology (DP) workflows to obtain whole slide image (WSI) files for diagnostic purposes has increased in the last few years. The increasing performance of technical components and the Food and Drug Administration (FDA) approval of systems for primary diagnosis led to increased interest in applying DP workflows. However, despite this revolutionary transition, real world data suggest that a fully digital approach to the histological workflow has been implemented in only a minority of pathology laboratories. The objective of this study is to facilitate the implementation of DP workflows in pathology laboratories, helping those involved in this process of transformation to identify: (a) the scope and the boundaries of the DP transformation; (b) how to introduce automation to reduce errors; (c) how to introduce appropriate quality control to guarantee the safety of the process and (d) the hardware and software needed to implement DP systems inside the pathology laboratory. The European Society of Digital and Integrative Pathology (ESDIP) provided consensus-based recommendations developed through discussion among members of the Scientific Committee. The recommendations are thus based on the expertise of the panel members and on the agreement obtained after virtual meetings. Prior to publication, the recommendations were reviewed by members of the ESDIP Board. The recommendations comprehensively cover every step of the implementation of the digital workflow in the anatomic pathology department, emphasizing the importance of interoperability, automation and tracking of the entire process before the introduction of a scanning facility. Compared to the available national and international guidelines, the present document represents a practical, handy reference for the correct implementation of the digital workflow in Europe.publishedVersio