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Chromatix: a differentiable, GPU-accelerated wave-optics library.

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Τίτλος: Chromatix: a differentiable, GPU-accelerated wave-optics library.
Συγγραφείς: Deb D; HHMI Janelia Research Campus, Ashburn, VA, USA. debd@janelia.hhmi.org., Both GJ; HHMI Janelia Research Campus, Ashburn, VA, USA. bothg@janelia.hhmi.org., Bezzam E; Audiovisual Communications Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland., Kohli A; Department of Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley, CA, USA., Yang S; Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA., Chaware A; Department of Biomedical Engineering, Duke University, Durham, NC, USA., Allier C; HHMI Janelia Research Campus, Ashburn, VA, USA., Cai C; Department of Applied Physical Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Anderberg G; Department of Radiology, University of Chicago, Chicago, IL, USA., Eybposh MH; Department of Applied Physical Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Schneider MC; HHMI Janelia Research Campus, Ashburn, VA, USA., Heintzmann R; Leibniz Institute of Photonic Technology, Jena, Germany.; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Jena, Germany., Rivera-Sanchez FA; Imaging Physics, Faculty of Applied Sciences, Technische Universiteit Delft, Delft, The Netherlands.; Advanced Research Center for Nanolithography (ARCNL), Amsterdam, The Netherlands., Simmerer C; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Meng G; Department of Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley, CA, USA.; Herbert Wertheim School of Optometry and Vision Science, University of California, Berkeley, CA, USA., Tormes-Vaquerano J; Department of Applied Physical Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Han S; Department of Applied Physics, Yale University, New Haven, CT, USA., Shanmugavel SC; Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA., Maruvada T; Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA., Yang X; Department of Biomedical Engineering, Duke University, Durham, NC, USA., Kim Y; Department of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea., Diederich B; Leibniz Institute of Photonic Technology, Jena, Germany., Joo C; Department of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea., Waller L; Department of Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley, CA, USA., Durr NJ; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Pégard NC; Department of Applied Physical Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Carolina Stress Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., La Rivière PJ; Department of Radiology, University of Chicago, Chicago, IL, USA., Horstmeyer R; Department of Biomedical Engineering, Duke University, Durham, NC, USA., Chowdhury S; Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA., Turaga SC; HHMI Janelia Research Campus, Ashburn, VA, USA. turagas@janelia.hhmi.org.
Πηγή: Nature methods [Nat Methods] 2026 Jul; Vol. 23 (7), pp. 1388-1398. Date of Electronic Publication: 2026 Jun 08.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
Imprint Name(s): Original Publication: New York, NY : Nature Pub. Group, c2004-
Ιατρικοί όροι (MeSH): Optics and Photonics*/methods , Microscopy*/methods , Image Processing, Computer-Assisted*/methods , Computer Graphics* , Software*, Holography ; Computer Simulation ; Algorithms
Περίληψη: Many current microscopy methods incorporate computational modeling as an integral part of the imaging process, either to solve inverse problems or optimize the optical system design itself. These methods often depend on differentiable optics simulations, yet no standardized framework exists, forcing computational optics researchers to repeatedly and independently implement simulations with limited reusability and performance. These common problems limit the potential impact of computational optics as a field. Here we present Chromatix: an open-source, graphics processing unit (GPU)-accelerated, differentiable wave-optics simulation library. Chromatix builds on JAX to democratize fast, parallelized simulation of diverse optical systems and expand the design space in computational optics. Chromatix standardizes a growing collection of optical elements and propagation methods allowing a broad range of applications, which we demonstrate here for snapshot microscopy, holography and phase retrieval. We demonstrate speed improvements of 2-6 times on a single GPU and up to 22 times on 8 GPUs.
(© 2026. The Author(s).)
Competing Interests: Competing interests: The authors declare no competing interests.
Σχόλια: Update of: bioRxiv. 2026 Mar 25:2025.04.29.651152. doi: 10.1101/2025.04.29.651152.. (PMID: 41929201)
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Grant Information: R35 GM155424 United States GM NIGMS NIH HHS; No.2023R1A2C3004040 National Research Foundation of Korea (NRF)
Entry Date(s): Date Created: 20260608 Date Completed: 20260709 Latest Revision: 20260726
Update Code: 20260726
PubMed Central ID: PMC13345901
DOI: 10.1038/s41592-026-03121-x
PMID: 42260310
Βάση Δεδομένων: MEDLINE
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Nature+Pub%2E+Group%22">Nature Pub. Group </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>101215604 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1548-7105 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2215487091%22">15487091 </searchLink><i>NLM ISO Abbreviation: </i>Nat Methods <i>Subsets: </i>MEDLINE
– Name: PublisherInfo
  Label: Imprint Name(s)
  Group: PubInfo
  Data: <i>Original Publication</i>: New York, NY : Nature Pub. Group, c2004-
– Name: SubjectMESH
  Label: MeSH Terms
  Group: Su
  Data: <searchLink fieldCode="MM" term="%22Optics+and+Photonics%22">Optics and Photonics*</searchLink>/<searchLink fieldCode="MM" term="%22Optics+and+Photonics+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Microscopy%22">Microscopy*</searchLink>/<searchLink fieldCode="MM" term="%22Microscopy+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Image+Processing%2C+Computer-Assisted%22">Image Processing, Computer-Assisted*</searchLink>/<searchLink fieldCode="MM" term="%22Image+Processing%2C+Computer-Assisted+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Computer+Graphics%22">Computer Graphics*</searchLink> <br /><searchLink fieldCode="MM" term="%22Software%22">Software*</searchLink><br /><searchLink fieldCode="MH" term="%22Holography%22">Holography</searchLink> ; <searchLink fieldCode="MH" term="%22Computer+Simulation%22">Computer Simulation</searchLink> ; <searchLink fieldCode="MH" term="%22Algorithms%22">Algorithms</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Many current microscopy methods incorporate computational modeling as an integral part of the imaging process, either to solve inverse problems or optimize the optical system design itself. These methods often depend on differentiable optics simulations, yet no standardized framework exists, forcing computational optics researchers to repeatedly and independently implement simulations with limited reusability and performance. These common problems limit the potential impact of computational optics as a field. Here we present Chromatix: an open-source, graphics processing unit (GPU)-accelerated, differentiable wave-optics simulation library. Chromatix builds on JAX to democratize fast, parallelized simulation of diverse optical systems and expand the design space in computational optics. Chromatix standardizes a growing collection of optical elements and propagation methods allowing a broad range of applications, which we demonstrate here for snapshot microscopy, holography and phase retrieval. We demonstrate speed improvements of 2-6 times on a single GPU and up to 22 times on 8 GPUs.<br /> (© 2026. The Author(s).)
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: Competing interests: The authors declare no competing interests.
– Name: Comment
  Label: Comments
  Group: Commnt
  Data: Update of: bioRxiv. 2026 Mar 25:2025.04.29.651152. doi: 10.1101/2025.04.29.651152.. (PMID: <searchLink fieldCode="PM" term="%2241929201%22">41929201)</searchLink>
– Name: Ref
  Label: References
  Group: RefInfo
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  Data: R35 GM155424 United States GM NIGMS NIH HHS; No.2023R1A2C3004040 National Research Foundation of Korea (NRF)
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  Data: <i>Date Created: </i>20260608 <i>Date Completed: </i>20260709 <i>Latest Revision: </i>20260726
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        Value: 10.1038/s41592-026-03121-x
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        StartPage: 1388
    Subjects:
      – SubjectFull: Holography
        Type: general
      – SubjectFull: Computer Simulation
        Type: general
      – SubjectFull: Algorithms
        Type: general
      – SubjectFull: Optics and Photonics methods
        Type: general
      – SubjectFull: Microscopy methods
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      – SubjectFull: Image Processing, Computer-Assisted methods
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              Text: 2026 Jul
              Type: published
              Y: 2026
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            – TitleFull: Nature methods
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