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pan-ASLM: Axially Swept Light Sheet Microscopy for Fast and High-Resolution Imaging of Expanded Samples.

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Paper

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The authors' code

MATLAB · 74 lines · 1.1 KB · no license

  2. fileName= "Composite_cellzstack10twocells";
  4. %im = tiffreadVolume('scan width 8 no sample.tiff');
  5. %im = tiffreadVolume('scan width 32 no sample.tiff');
  7. im = tiffreadVolume(fileName + ".tif");
  8. %%
  9. image = im(:,:, 49);
  10. figure()
  11. imshow(image,[]);
  14. %%
  16. frecImage = fftshift(fft2(double(image)));
  17. imshow(log(frecImage),[]);
  18. %%
  19. filterPoints = [239, 240, 241, 478, 885, 1123, 1124, 1361, 1362, 1840, 1841, 2078, 2079, 2080, 2723, 2724, 2725, 2961, 2962, 2963];
  22. frequencyFilter = ones(size(image));
  23. for ii = 1: length(filterPoints)
  24. frequencyFilter(filterPoints(ii),1601) = 0;
  25. end
  28. frecImageFiltered = frecImage.*frequencyFilter;
  29. %%
  31. imwrite(frequencyFilter(:,:),"frequencyFilter.tiff");
  33. %%
  34. imshow(log(frecImageFiltered),[]);
  36. %%
  38. filteredImage = abs(ifft2(ifftshift(frecImageFiltered)));
  39. figure()
  40. imshow((filteredImage),[])
  42. %%
  43. figure()
  44. imagesc(abs((frecImage)));
  45. colormap('gray')
  49. %%
  51. filteredImage = uint16(FrequencyFilter2D(im(:,:,:),frequencyFilter));
  53. %%
  54. figure()
  55. imshow(filteredImage(:,:,50),[])
  56. for ii = 2:2:320
  57. imwrite(filteredImage(:,:,ii),fileName + " ch2 filtered "+ string(ii) + ".tiff");
  58. end
  63. %%
  65. t = Tiff('myfile.tif','w');

2d_frequency_filtering.m at commit 97d0a01, no license · at the source

Overview

Authors: Hannahmariam T. Mekbib1,2, Lasse Pærgård Andersen2,3, Shuwen Zhang2, Jonathan Gulcicek4, Yuan Tian2, Jack R. Ross5, Mark D. Lessard2, Joerg Bewersdorf1,2,5,6,7
ORCID iDs: Yuan Tian, Joerg Bewersdorf
  1. Department of Biomedical Engineering, Yale University,New Haven, CT USA
  2. Department of Cell Biology, Yale School of Medicine,New Haven, CT USA
  3. DTU Health Tech, Technical University of Denmark,Kgs Lyngby, Denmark
  4. panluminate Inc., New Haven, CT USA
  5. Department of Physics, Yale University,New Haven, CT USA
  6. Nanobiology Institute, Yale University,West Haven, CT USA
  7. Kavli Institute for Neuroscience, Yale School of Medicine,New Haven, CT USA
Institutions: Yale University (United States); Technical University of Denmark (Denmark)
Journal: Npj imaging, volume 4, issue 1, article 16
Dates: received 17 August 2025; accepted 26 January 2026; published online 23 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s44303-026-00141-2 · PMID 41872457 · PMCID PMC13009474 · OpenAlex W7140094998
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: histology / microscopy (modality)
Methods: fMRI & imaging, Physiology & signal measures
Keywords: Biological techniques, Biophysics, Cell biology, Optics and photonics
Topic: Advanced Fluorescence Microscopy Techniques (Biophysics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Novo Nordisk Fonden (NNF20OC0059893); National Institute of Diabetes and Digestive and Kidney Diseases (R43DK137685); U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH) (R44MH128999); Wellcome Leap
Citations: not cited yet (Europe PMC); 39 references in the paper

Abstract

Expansion microscopy, a super-resolution fluorescence microscopy technique in which samples are expanded up to ~8000 times (after 20-fold expansion) their original volume, places high demands on the microscopes used to image the expanded samples. To reveal nanoscale cellular ultrastructure in meaningful sample volumes, the instruments need to feature a large field of view and working distance. Simultaneously, they need to offer a high three-dimensional resolution to avoid counteracting the resolution improvement achieved by the expansion process. Here, we present pan-ASLM, a high resolution, large field-of-view light-sheet microscope developed for expanded samples, based on the Axially Swept Light Sheet Microscopy (ASLM) technique. pan-ASLM allows imaging over a 640 x 640 µm2 field of view with lateral and axial resolutions of 586 and 428 nm, respectively, and features an image acquisition speed of up to 20 fps (183 Mvoxels/sec). It offers ~1200× higher imaging speed, a ~7× larger field of view, and ~2× better axial resolution than the standard confocal microscopes typically used for expanded samples. We validate the new microscope design through imaging of pan-expanded HeLa cells as well as mouse kidney and brain tissue.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

lasselpk/pan-ASLM

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 97d0a0102db8cbe1a6ead8d5b7feb725156701f5, 14 August 2025
Languages: MATLAB (6)
Size: 311 files, 6 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, documentation
Not found: license file, CITATION.cff, environment file, tests, continuous integration
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
7 files
At the source: github.com/lasselpk/pan-ASLM/

Code availability

The microscope control software is available at https://github.com/lasselpk/pan-ASLM/.

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 6 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

The data presented in this paper are deposited to BioImage Archive39 with accession number S-BIAD2357.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 4 keywords, 4 funders, 38 references.

Cite

This paper

Mekbib, H. T., Andersen, L. P., Zhang, S., Gulcicek, J., Tian, Y., Ross, J. R., Lessard, M. D., & Bewersdorf, J. (2026). pan-ASLM: Axially Swept Light Sheet Microscopy for Fast and High-Resolution Imaging of Expanded Samples. Npj imaging, 4(1), 16. https://doi.org/10.1038/s44303-026-00141-2

BibTeX

@article{mekbib2026pan,
author = {Mekbib, Hannahmariam T. and Andersen, Lasse Pærgård and Zhang, Shuwen and Gulcicek, Jonathan and Tian, Yuan and Ross, Jack R. and Lessard, Mark D. and Bewersdorf, Joerg},
title = {{pan-ASLM: Axially Swept Light Sheet Microscopy for Fast and High-Resolution Imaging of Expanded Samples}},
journal = {Npj imaging},
year = {2026},
month = mar,
volume = {4},
number = {1},
pages = {16},
publisher = {Springer Science+Business Media},
issn = {2948-197X},
doi = {10.1038/s44303-026-00141-2},
url = {https://doi.org/10.1038/s44303-026-00141-2},
pmid = {41872457},
pmcid = {PMC13009474}
}

RIS

TY - JOUR
AU - Mekbib, Hannahmariam T.
AU - Andersen, Lasse Pærgård
AU - Zhang, Shuwen
AU - Gulcicek, Jonathan
AU - Tian, Yuan
AU - Ross, Jack R.
AU - Lessard, Mark D.
AU - Bewersdorf, Joerg
TI - pan-ASLM: Axially Swept Light Sheet Microscopy for Fast and High-Resolution Imaging of Expanded Samples
T2 - Npj imaging
J2 - Npj Imaging
PY - 2026
DA - 2026/03/23
VL - 4
IS - 1
SP - 16
SN - 2948-197X
PB - Springer Science+Business Media
DO - 10.1038/s44303-026-00141-2
UR - https://doi.org/10.1038/s44303-026-00141-2
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s44303-026-00141-2",
"type": "article-journal",
"title": "pan-ASLM: Axially Swept Light Sheet Microscopy for Fast and High-Resolution Imaging of Expanded Samples",
"container-title": "Npj imaging",
"author": [
{
"family": "Mekbib",
"given": "Hannahmariam T."
},
{
"family": "Andersen",
"given": "Lasse Pærgård"
},
{
"family": "Zhang",
"given": "Shuwen"
},
{
"family": "Gulcicek",
"given": "Jonathan"
},
{
"family": "Tian",
"given": "Yuan"
},
{
"family": "Ross",
"given": "Jack R."
},
{
"family": "Lessard",
"given": "Mark D."
},
{
"family": "Bewersdorf",
"given": "Joerg"
}
],
"container-title-short": "Npj Imaging",
"volume": "4",
"issue": "1",
"page": "16",
"DOI": "10.1038/s44303-026-00141-2",
"PMID": "41872457",
"PMCID": "PMC13009474",
"ISSN": "2948-197X",
"publisher": "Springer Science+Business Media",
"URL": "https://doi.org/10.1038/s44303-026-00141-2",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
23
]
]
}
}

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