Published March 18, 2025 | Version v3
Dataset Open

Training Images for "ImmuNet" Convolutional Neural Network

Creators

  • 1. Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
  • 2. Data Science group, Institute for Computing and Information Sciences, Radboud University, Nijmegen, The Netherlands
  • 3. Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands

Description

This dataset contains all annotations and images for training the machine learning architecture presented in this manscript:

Shabaz Sultan, Mark A. J. Gorris, Lieke L. van der Woude, Franka Buytenhuijs, Evgenia Martynova, Sandra van Wilpe, Kiek Verrijp, Carl G. Figdor, I. Jolanda M. de Vries, Johannes Textor:
ImmuNet: a segmentation-free machine learning pipeline for immune landscape phenotyping in tumors by multiplex imaging.
Biology Methods and Protocols 10(1), bpae094, 2025. doi: 10.1093/biomethods/bpae094

The .tar.gz file contains several multichannel images stored as TIFF files, and arranged in a folder structure that is convenient for matching the files to the annotations provided in the .json.gz file. We also provide an .h5 file that contains the final trained network that was used to generate the figures in this manuscript.

Further information on the data can be found in the manuscript cited above. Instructions on how to use the annotations and the code can be found on our GitHub page at: https://github.com/jtextor/immunet

Notes

Additional funding information: JT and SS were supported by the Dutch Cancer Society - Alpe d'HuZes foundation (grant 10620). JT and FB were supported by NWO grant VI.Vidi.192.084. MG, LvdW, KV, and CF were supported by Dutch Cancer Society grants 10673 and 2017-8244. CF was also supported by a grant from Oncode Institute. EM was supported by a grant from the Hanarth Fonds (to JT).

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Additional details

Related works

Is supplement to
Preprint: 10.1101/2021.10.22.464548 (DOI)
Software: https://github.com/jtextor/immunet (URL)

Funding

European Commission
ARTimmune - Programmable ARTificial immune systems to fight cancer 834618