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TAPAS: Towards Automated Processing and Analysis of multi-dimensional bioimage data.

Jean-François Gilles1, Thomas Boudier1,2

  • 1Sorbonne Université, Institut de Biologie Paris-Seine, IBPS, Paris, France.

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|September 28, 2021
PubMed
Summary
This summary is machine-generated.

We developed TAPAS (Towards an Automated Processing and Analysis System), a user-friendly platform for microscopy image analysis. This system enables reproducible, standardized batch processing of image data with minimal programming, facilitating data sharing and reuse.

Keywords:
FijiImage processingImageJOMEROautomationimage analysis

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Area of Science:

  • Microscopy and Image Analysis
  • Bioinformatics
  • Scientific Software Development

Background:

  • Reproducible quantitative analysis is crucial in modern microscopy.
  • Standardized, shareable, and reusable image processing systems are needed.
  • Current systems often require significant programming expertise.

Purpose of the Study:

  • To develop TAPAS (Towards an Automated Processing and Analysis System) for easy description and exchange of image processing workflows.
  • To provide a user-friendly system for batch processing and analysis of microscopy images.
  • To reduce the programming barrier for researchers in image analysis.

Main Methods:

  • Developed TAPAS, a system utilizing simple text files for defining processing protocols.
  • Integrated an extensive set of 60 modules, largely based on the 3D ImageJ Suite.
  • Implemented a wizard (TAPAS menu) to guide users in protocol design with default parameter options.
  • Enabled application of protocols to locally stored or OMERO database-hosted image sets.

Main Results:

  • TAPAS allows users to create and execute image processing and analysis workflows with minimal coding.
  • The system supports batch processing of images through standardized, shareable protocols.
  • A comprehensive set of modules and a user-friendly interface streamline the analysis pipeline.

Conclusions:

  • TAPAS offers an accessible solution for reproducible and automated image analysis in microscopy.
  • The system enhances data sharing and reuse by standardizing processing workflows.
  • TAPAS empowers researchers to perform complex image analyses without extensive programming knowledge.