An integrative web-based software tool for multi-dimensional pathology whole-slide image analytics

Alice Shen, Fusheng Wang, Saptarshi Paul, Divya Bhuvanapalli, Jacob Alayof, Alton B. Farris, George Teodoro, Daniel J. Brat, Jun Kong*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Objective. In the era of precision medicine, human tumor atlas-oriented studies have been significantly facilitated by high-resolution, multi-modal tissue based microscopic pathology image analytics. To better support such tissue-based investigations, we have developed Digital Pathology Laboratory (DPLab), a publicly available web-based platform, to assist biomedical research groups, non-technical end users, and clinicians for pathology whole-slide image visualization, annotation, analysis, and sharing via web browsers. Approach. A major advancement of this work is the easy-to-follow methods to reconstruct three-dimension (3D) tissue image volumes by registering two-dimension (2D) whole-slide pathology images of serial tissue sections stained by hematoxylin and eosin (H&E), and immunohistochemistry (IHC). The integration of these serial slides stained by different methods provides cellular phenotype and pathophysiologic states in the context of a 3D tissue micro-environment. DPLab is hosted on a publicly accessible server and connected to a backend computational cluster for intensive image analysis computations, with results visualized, downloaded, and shared via a web interface. Main results. Equipped with an analysis toolbox of numerous image processing algorithms, DPLab supports continued integration of community-contributed algorithms and presents an effective solution to improve the accessibility and dissemination of image analysis algorithms by research communities. Significance. DPLab represents the first step in making next generation tissue investigation tools widely available to the research community, enabling and facilitating discovery of clinically relevant disease mechanisms in a digital 3D tissue space.

Original languageEnglish (US)
Article number224001
JournalPhysics in Medicine and Biology
Issue number22
StatePublished - Nov 21 2022


  • digital pathology
  • high performance computing
  • image analysis
  • image registration
  • web computing
  • whole slide images

ASJC Scopus subject areas

  • Radiological and Ultrasound Technology
  • Radiology Nuclear Medicine and imaging


Dive into the research topics of 'An integrative web-based software tool for multi-dimensional pathology whole-slide image analytics'. Together they form a unique fingerprint.

Cite this