Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

ZeroCostDL4Mic: an open platform to use Deep-Learning in Microscopy

View ORCID ProfileLucas von Chamier, View ORCID ProfileRomain F. Laine, Johanna Jukkala, View ORCID ProfileChristoph Spahn, Daniel Krentzel, Elias Nehme, View ORCID ProfileMartina Lerche, View ORCID ProfileSara Hernández-Pérez, View ORCID ProfilePieta K. Mattila, View ORCID ProfileEleni Karinou, View ORCID ProfileSéamus Holden, Ahmet Can Solak, View ORCID ProfileAlexander Krull, View ORCID ProfileTim-Oliver Buchholz, View ORCID ProfileMartin L. Jones, View ORCID ProfileLoïc A Royer, View ORCID ProfileChristophe Leterrier, View ORCID ProfileYoav Shechtman, View ORCID ProfileFlorian Jug, View ORCID ProfileMike Heilemann, View ORCID ProfileGuillaume Jacquemet, View ORCID ProfileRicardo Henriques
doi: https://doi.org/10.1101/2020.03.20.000133
Lucas von Chamier
1MRC-Laboratory for Molecular Cell Biology, University College London, London, UK, ChamierLucas
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lucas von Chamier
Romain F. Laine
1MRC-Laboratory for Molecular Cell Biology, University College London, London, UK, ChamierLucas
2The Francis Crick Institute, London, UK, LaineBioImaging
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Romain F. Laine
Johanna Jukkala
3Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland, Liehuletti
4Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland, miCHRIScopy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christoph Spahn
5Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany, DanielKrentzel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christoph Spahn
Daniel Krentzel
6Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK, martina_lerche
7Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK, sara_mattilalab
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Elias Nehme
8Department of Electrical Engineering, Technion - Israel Institute of Technology, Haifa, Israel, mattilalab
9Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel, Kar__El
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Martina Lerche
3Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland, Liehuletti
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Martina Lerche
Sara Hernández-Pérez
3Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland, Liehuletti
10Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Finland, seamus_holden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sara Hernández-Pérez
Pieta K. Mattila
3Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland, Liehuletti
10Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Finland, seamus_holden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Pieta K. Mattila
Eleni Karinou
11Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK, _ahmetcansolak
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Eleni Karinou
Séamus Holden
11Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK, _ahmetcansolak
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Séamus Holden
Ahmet Can Solak
12Chan Zuckerberg Biohub, San Francisco, CA, USA, sagzehn
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alexander Krull
13Center for Systems Biology Dresden (CSBD), Dresden, Germany, tibuch_
14Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany, martinjones78
15Max Planck Institute for Physics of Complex Systems, Dresden, Germany, loicaroyer
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alexander Krull
Tim-Oliver Buchholz
13Center for Systems Biology Dresden (CSBD), Dresden, Germany, tibuch_
14Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany, martinjones78
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tim-Oliver Buchholz
Martin L. Jones
6Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK, martina_lerche
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Martin L. Jones
Loïc A Royer
12Chan Zuckerberg Biohub, San Francisco, CA, USA, sagzehn
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Loïc A Royer
Christophe Leterrier
16Aix Marseille Universite, CNRS, INP UMR7051, NeuroCyto, Marseille, France, @christlet
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christophe Leterrier
Yoav Shechtman
9Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel, Kar__El
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yoav Shechtman
Florian Jug
13Center for Systems Biology Dresden (CSBD), Dresden, Germany, tibuch_
14Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany, martinjones78
17Fondatione Human Technopole, Milano, Italy, ShechtmanLab, florianjug
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Florian Jug
Mike Heilemann
5Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany, DanielKrentzel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mike Heilemann
Guillaume Jacquemet
3Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland, Liehuletti
4Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland, miCHRIScopy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Guillaume Jacquemet
  • For correspondence: guillaume.jacquemet@abo.fi rjhenriques@igc.gulbenkian.pt
Ricardo Henriques
1MRC-Laboratory for Molecular Cell Biology, University College London, London, UK, ChamierLucas
2The Francis Crick Institute, London, UK, LaineBioImaging
18Instituto Gulbenkian de Ciência, Oeiras, Portugal, guijacquemet, HenriquesLab
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ricardo Henriques
  • For correspondence: guillaume.jacquemet@abo.fi rjhenriques@igc.gulbenkian.pt
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

The resources and expertise needed to use Deep Learning (DL) in bioimaging remain significant barriers for most laboratories. We present https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki, a platform simplifying access to DL by exploiting the free, cloud-based computational resources of Google Colab. https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki allows researchers to train, evaluate, and apply key DL networks to perform tasks including segmentation, detection, denoising, restoration, resolution enhancement and image-to-image translation. We demonstrate the application of the platform to study multiple biological processes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Minor corrections to abstract and movies

  • https://github.com/HenriquesLab/ZeroCostDL4Mic

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted August 17, 2020.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
ZeroCostDL4Mic: an open platform to use Deep-Learning in Microscopy
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
ZeroCostDL4Mic: an open platform to use Deep-Learning in Microscopy
Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K. Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L. Jones, Loïc A Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques
bioRxiv 2020.03.20.000133; doi: https://doi.org/10.1101/2020.03.20.000133
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
ZeroCostDL4Mic: an open platform to use Deep-Learning in Microscopy
Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K. Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L. Jones, Loïc A Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques
bioRxiv 2020.03.20.000133; doi: https://doi.org/10.1101/2020.03.20.000133

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (2440)
  • Biochemistry (4803)
  • Bioengineering (3340)
  • Bioinformatics (14724)
  • Biophysics (6658)
  • Cancer Biology (5188)
  • Cell Biology (7455)
  • Clinical Trials (138)
  • Developmental Biology (4378)
  • Ecology (6904)
  • Epidemiology (2057)
  • Evolutionary Biology (9943)
  • Genetics (7357)
  • Genomics (9550)
  • Immunology (4583)
  • Microbiology (12730)
  • Molecular Biology (4960)
  • Neuroscience (28422)
  • Paleontology (199)
  • Pathology (810)
  • Pharmacology and Toxicology (1400)
  • Physiology (2031)
  • Plant Biology (4521)
  • Scientific Communication and Education (980)
  • Synthetic Biology (1305)
  • Systems Biology (3922)
  • Zoology (731)