TissueWand, a rapid histopathology annotation tool

Lindvall, MartinLinköpings universitet,Medie- och Informationsteknik,Tekniska fakulteten,Centrum för medicinsk bildvetenskap och visualisering, CMIV,Sectra AB (author)

Background: Recent advancements in machine learning (ML) bring great possibilities for the development of tools to assist with diagnostic tasks within histopathology. However, these approaches typically require a large amount of ground truth training data in the form of image annotations made by human experts. As such annotation work is a very time-consuming task, there is a great need for tools that can assist in this process, saving time while not sacrificing annotation quality. Methods: In an iterative design process, we developed TissueWand – an interactive tool designed for efficient annotation of gigapixel-sized histopathological images, not being constrained to a predefined annotation task. Results: Several findings regarding appropriate interaction concepts were made, where a key design component was semi-automation based on rapid interaction feedback in a local region. In a user study, the resulting tool was shown to cause substantial speed-up compared to manual work while maintaining quality. Conclusions: The TissueWand tool shows promise to replace manual methods for early stages of dataset curation where no task-specific ML model yet exists to aid the effort.

Sanner, AlexanderSectra AB, Research Department, Linköping, Sweden (author)
Petré, FredrikSectra AB, Research Department, Linköping, Sweden (author)
Lindman, Karin,1980-Linköpings universitet,Avdelningen för neurobiologi,Medicinska fakulteten,Region Östergötland, Klinisk patologi(Swepub:liu)karsk31 (author)
Treanor, Darren,1974-Linköpings universitet,Avdelningen för inflammation och infektion,Medicinska fakulteten,Centrum för medicinsk bildvetenskap och visualisering, CMIV,Region Östergötland, Klinisk patologi,University of Leeds, Leeds, UK(Swepub:liu)dartr72 (author)
Lundström, Claes,1973-Linköpings universitet,Medie- och Informationsteknik,Tekniska fakulteten,Centrum för medicinsk bildvetenskap och visualisering, CMIV,Sectra AB(Swepub:liu)clalu03 (author)
Löwgren, Jonas,1964-Linköpings universitet,Medie- och Informationsteknik,Tekniska fakulteten(Swepub:liu)jonlo66 (author)
Linköpings universitetMedie- och Informationsteknik (creator_code:org_t)

In:Journal of Pathology Informatics: Medknow Publications11:272229-50892153-3539

By the author/editor: Lindvall, Martin; Sanner, Alexande ...; Petré, Fredrik; Lindman, Karin, ...; Treanor, Darren, ...; Lundström, Claes ...; show more...; Löwgren, Jonas, ...; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Human Computer I ...

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