BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data

Research output: Contribution to journalArticle

Abstract

SUMMARY: Modern bioimaging and related areas such as sensor technology have undergone tremendous development over the last few years. As a result, contemporary imaging techniques, particularly electron microscopy (EM) and light sheet microscopy, can frequently generate datasets attaining sizes of several terabytes (TB). As a consequence, even seemingly simple data operations such as cropping, chromatic- and drift-corrections and even visualisation, poses challenges when applied to thousands of time points or tiles. To address this we developed BigDataProcessor2-a Fiji plugin facilitating processing workflows for TB sized image datasets.

AVAILABILITY AND IMPLEMENTATION: BigDataProcessor2 is available as a Fiji plugin via the BigDataProcessor update site. The application is implemented in Java and the code is publicly available on GitHub (https://github.com/bigdataprocessor/bigdataprocessor2).

Details

Authors
  • Christian Tischer
  • Ashis Ravindran
  • Sabine Reither
  • Nicolas Chiaruttini
  • Rainer Pepperkok
  • Nils Norlin
Organisations
External organisations
  • European Molecular Biology Laboratory Heidelberg
  • Heidelberg University
  • Swiss Federal Institute of Technology
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Software Engineering
  • Information Systems, Social aspects
Original languageEnglish
JournalBioinformatics (Oxford, England)
Publication statusE-pub ahead of print - 2021 Feb 17
Publication categoryResearch
Peer-reviewedYes