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Image analysis in Galaxy,

is that even possible?

Beatriz Serrano-Solano

European Galaxy Team

University of Freiburg

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Image Data Access

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IDR/OMERO

Download

tool

Define ROI

Local OMERO instances accessible

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Image Analysis

Tools

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https://imaging.usegalaxy.eu

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Workflows

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Exemplary workflow from EOSC-Life

Goal

​

Looking at phenotypes to find potential regulators of nucleolus biology

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Data

Conversion & Submission

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OME-zarr

  • Standard image format
  • Representation of n-dimensional data
  • Binary data + metadata
  • Natively cloud-compatible
  • Data access chunked and multiscale
  • Higher access speed, especially for remotely stored datasets
  • 8 TB in object store
  • Fast inspection

Bugra Özdemir �Image Data Specialist

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Parameters

Data

OME-zarr support in Galaxy

Data conversion

  • Proprietary file format
  • From
    • Local storage
    • BIA

Data submission

  • ftp2BIA
  • ascp2BIA

Bugra Özdemir �Image Data Specialist

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Open and FAIR Image data storage

Standardized file

and Metadata formats

Cloud compatible image analysis workflows

Large and information-rich image data

Bugra Özdemir �Image Data Specialist

Isabel Kemmer �FAIR Image Data Steward

Slide adapted from Aastha Mathur

Image data submission to open repositories

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Training

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Training materials

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Tracking

Dividing nuclei of one mitosis of a syncytial blastoderm stage Drosophila embryo

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Interested?

Register your interest:

https://bit.ly/imaging-galaxy

@BSerranoSolano

beatrizserrano

beatrizserrano.galaxy@gmail.com

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Thank you