Skip to main content

Advertisement

SpringerLink
Log in

CLIJ: GPU-accelerated image processing for everyone

  • Correspondence
  • Published:

From Nature Methods

View current issue Submit your manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1: CLIJ performance overview.

Data availability

All data to support our findings are available through the links listed in Supplementary Table 2. Further details can be found in the Reporting Summary.

Code availability

CLIJ is available as Supplementary Software 2. The fully open source code is available through the links listed in Supplementary Table 2. Updated versions of the software can also be found at https://clij.github.io. Further details can be found in the Reporting Summary.

References

  1. Preibisch, S. et al. Nat. Methods 11, 645–648 (2014).

    Article  CAS  Google Scholar 

  2. Laine, R. F. et al. J. Phys. Appl. Phys. 52, 163001 (2019).

    Article  CAS  Google Scholar 

  3. Culley, S. et al. Nat. Methods 15, 263–266 (2018).

    Article  CAS  Google Scholar 

  4. Weigert, M. et al. Nat. Methods 15, 1090–1097 (2018).

    Article  CAS  Google Scholar 

  5. Falk, T. et al. Nat. Methods 16, 67–70 (2019).

    Article  CAS  Google Scholar 

  6. Schmid, B. et al. Nat. Methods 16, 278–280 (2019).

    Article  CAS  Google Scholar 

  7. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. Nat. Methods 9, 671–675 (2012).

    Article  CAS  Google Scholar 

  8. Schindelin, J. et al. Nat. Methods 9, 676–682 (2012).

    Article  CAS  Google Scholar 

  9. The Khronos Group. The open standard for parallel programming of heterogeneous systems https://www.khronos.org/opencl/ (2019).

  10. Rueden, C. T. et al. BMC Bioinform. 18, 529 (2017).

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank everybody who helped developing and testing CLIJ. In particular thanks goes to A. Herbert (University of Sussex), B. C. Vellutini (MPI-CBG), C. Rueden (UW-Madison LOCI), D. Krunic (DKFZ), D. J. White (GE), G. G. Martins (IGC), S. Culley (LMCB MRC), G. Cardone (MPI Biochem), J. Brocher (Biovoxxel), J. Girstmair (MPI-CBG), J. Gluch (Fraunhofer IKTS), K. Miura, L. Thomas (Acquifer), N. Stuurman (UCSF), P. Haub, P. Rajasekhar (Monash University), T. Pietzsch (MPI-CBG), W. Adams (VU Biophotonics). R.H. was supported by the German Federal Ministry of Research and Education (BMBF) under the code 031L0044 (Sysbio II) and D.S. received support from the German Research Foundation (DFG) under the code JU3110/1-1. P.T. was supported by the European Regional Development Fund in the IT4Innovations national supercomputing center-path to exascale project, project number CZ.02.1.01/0.0/0.0/16_013/0001791 within the Operational Programme Research, Development and Education.

Author information

Author notes

  1. Peter Steinbach

    Present address: Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany

  2. These authors contributed equally: Robert Haase, Loic A. Royer.

Authors and Affiliations

  1. Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany

    Robert Haase, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug & Eugene W. Myers

  2. Center for Systems Biology Dresden, Dresden, Germany

    Robert Haase, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug & Eugene W. Myers

  3. Chan Zuckerberg Biohub, San Francisco, CA, USA

    Loic A. Royer

  4. IT4Innovations, VŠB - Technical University of Ostrava, Ostrava-Poruba, Czech Republic

    Pavel Tomancak

Authors
  1. Robert Haase
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Loic A. Royer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peter Steinbach
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Deborah Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Alexandr Dibrov
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Uwe Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Martin Weigert
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Nicola Maghelli
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Pavel Tomancak
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Florian Jug
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Eugene W. Myers
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

R.H. and L.A.R initiated the research. R.H., L.A.R., P.S, D.S., A.D., U.S. and M.W. wrote the source code of CLIJ. R.H. and N.M. performed the image acquisition of the example data. E.W.M. supervised the project. R.H., L.A.R., U.S., M.W., P.T. and F.J. wrote the manuscript with input from all co-authors.

Corresponding authors

Correspondence to Robert Haase or Loic A. Royer.

Ethics declarations

Competing interests

The authors declare no competing interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–7, Supplementary Tables 1 and 2, and Supplementary Notes 1 and 2.

Reporting Summary

Supplementary Video 1

Results from processed time-lapse for benchmarking workflow. A video showing a developing Drosophila embryo in maximum projection and cylinder maximum projection with marked spot detection and spot count plotted over time.

Supplementary Software 1

CLIJ usage examples: Scripts demonstrating CLIJ in various ImageJ/Fiji compatible programming languages.

Supplementary Software 2

Reviewed version of CLIJ software.

Source data

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Haase, R., Royer, L.A., Steinbach, P. et al. CLIJ: GPU-accelerated image processing for everyone. Nat Methods 17, 5–6 (2020). https://doi.org/10.1038/s41592-019-0650-1

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41592-019-0650-1

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation