title: Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.
abstract: BACKGROUND
  Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools.
  
  
  METHODS
  Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries.
  
  
  RESULTS
  We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format.
  
  
  CONCLUSIONS
  Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.
authors.forename: David
authors.initials: D
authors.lastname: Ameisen
authors.forename: Christophe
authors.initials: C
authors.lastname: Deroulers
authors.forename: Valérie
authors.initials: V
authors.lastname: Perrier
authors.forename: Fatiha
authors.initials: F
authors.lastname: Bouhidel
authors.forename: Maxime
authors.initials: M
authors.lastname: Battistella
authors.forename: Luc
authors.initials: L
authors.lastname: Legrès
authors.forename: Anne
authors.initials: A
authors.lastname: Janin
authors.forename: Philippe
authors.initials: P
authors.lastname: Bertheau
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Yunès
mesh_terms: D006801:Humans; D007090:Image Interpretation, Computer-Assisted; D046609:Libraries, Digital; D008853:Microscopy / Q000379:methods; D010340:Pathology, Surgical / Q000379:methods*; D012984:Software; D019113:Telepathology / Q000379:methods*; D013997:Time Factors; D057188:Workflow