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Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution imaging.

Code ↔ Paper

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  1. [1] § STAR★Methods › Quantification and statistical analysis › BAMM unmixing ↔ BAMM/Code/BAMM_blind.m, the whole file · a weak match · score 0.57 · negative matrix factorization, bleaching curves, reshaped, BAMM, algorithm, intensity

Paper

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The authors' code

MATLAB · 82 lines · 2.5 KB · no license · 1 match

  1. % BAMM unmixing using non-negative matrix factorization
  2. % Written by Antony Orth, RMIT University, August 8 2018.
  3. % Citation:
  4. % Antony Orth, Richik N. Ghosh, Emma R. Wilson, Timothy Doughney, Hannah Brown, Philipp Reineck, Jeremy G. Thompson, and Brant C. Gibson, "Super-multiplexed fluorescence microscopy via photostability contrast," Biomed. Opt. Express 9, 2943-2954 (2018)
  6. function [imdmm, H]=BAMM_blind(a2_L1,k,nrep,flg)
  8. % k is the expected number of components to unmix. k=2 or 3.
  10. % a2_L1 is 3-dimensional matrix of size N x M x T contianing the bleaching
  11. % movie. Should have less than 200 frames.
  13. % nrep is the number of replicates of nnmf to run. Typically between 1-25.
  15. % flg is a flag. flg=0 for regular nnmf (bleaching curve must be positive everywhere);
  16. % flg=1 for non-decreasing nnmf (bleaching curve can never increase with time).
  18. % For k=3, flg=1 is usually required for physically sensible results.
  20. im2=reshape(a2_L1,size(a2_L1,1)*size(a2_L1,2),size(a2_L1,3)); % reshaping movie data
  22. opt = statset('Maxiter',100,'Display','final'); % settings for nnmf
  24. %%%%Non-negative matrix factorization (nnmf), requires Statistics and Machine
  25. %%%%Learning toolbox
  27. if flg==1
  28. [pc1,H]=nnmf_decrease(im2,k,'algorithm','als','replicates',nrep,'options',opt);
  29. elseif flg==0
  30. [pc1,H]=nnmf(im2,k,'algorithm','als','replicates',nrep,'options',opt);
  31. end
  34. imdmm=reshape(pc1,size(a2_L1,1),size(a2_L1,2),k); %reshaping output of nnmf into an image
  36. imdmm(:,:,1)=imdmm(:,:,1)*H(1,1); %normalizing component 1
  37. imdmm(:,:,2)=imdmm(:,:,2)*H(2,1); % normalizing component 2
  39. if k<3
  40. imdmm(:,:,3)=0; %setting the third component to 0 if there are only 2 components
  41. elseif k==3
  42. imdmm(:,:,3)=imdmm(:,:,3)*H(3,1); % normalizing component 3, if there is one
  43. end
  45. for nn=1:size(H,1)
  46. H(nn,:)=H(nn,:)/H(nn,1);
  47. end
  49. % figure;
  50. % imshow(squeeze(1*imdmm(:,:,[1 2 3]))); %display unmixed image
  51. % title('Unmixed image - no normalization')
  52. %
  53. % figure;
  54. % plot(H(1,:),'-r','LineWidth',2); %plot the estimated bleaching curves
  55. % hold on
  56. % plot(H(2,:),'-g','LineWidth',2);
  57. %
  58. % if size(H,1)==3
  59. % hold on
  60. % plot(H(3,:),'-b','LineWidth',2);
  61. % end
  62. %
  63. % xlabel('Frame #'); % Label the graph
  64. % ylabel('Intensity (A.U.)')
  65. % title('Bleaching components')
  66. %
  67. % imdmm1=norm_chn1(imdmm);
  68. %
  69. % figure;
  70. % imshow(imdmm1);
  71. % title('Unmixed image - channels normalized')
  73. end
  75. % %function that normalizes the maximum value of each channel to 1.
  76. % function im=norm_chn1(im0)
  77. % for n=1:size(im0,3)
  78. % tmp=im0(:,:,n);
  79. % tmp=tmp/max(tmp(:));
  80. % im(:,:,n)=tmp;
  81. % end
  82. % end

BAMM_blind.m at commit e6819a0, no license · at the source

Overview

Authors: Olumayowa Fakorede1,2,3, Zhien Rong1,2,3, Ruizhao Wang1,2,3, Stavrini Papadaki1,2,3, Xinyue Wang4, Jiayue Cao1,2,3, Fedor V Subach5, Reinhard W Köster4, Kazuhiko Namikawa4, Kiryl D Piatkevich1,2,3
ORCID iDs: Kiryl D Piatkevich
  1. School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
  2. Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
  3. Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
  4. Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
  5. Complex of NBICS Technologies, National Research Center ‘Kurchatov Institute’, Moscow, Russia
Institutions: Westlake University (China); Technische Universität Braunschweig (Germany); Kurchatov Institute (Russia)
Journal: Cell reports methods, volume 6, issue 7, article 101471
Dates: received 24 March 2025; accepted 1 May 2026; published online 29 May 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.crmeth.2026.101471 · PMID 42214338 · PMCID PMC13390083 · OpenAlex W7162787768
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), human (organism), mouse (organism), zebrafish (organism), C. elegans (organism), cellular / molecular (subfield)
Methods: Evoked potentials, Machine learning, fMRI & imaging
Keywords: far-red fluorescent proteins, multiplexed imaging, super-resolution microscopy, fluorescence lifetime imaging, temporal domain multiplexing
MeSH: Luminescent Proteins*, Animals, Caenorhabditis elegans, Humans, Mice, Microscopy, Fluorescence, Photobleaching, Red Fluorescent Protein, Zebrafish (* major topic)
Topic: Advanced Fluorescence Microscopy Techniques (Biophysics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Natural Science Foundation of China (32571589); Westlake University; National Natural Science Foundation of China National Outstanding Youth Science Fund Project (W2432024); National Research Council Canada
Citations: not cited yet (Europe PMC); 32 references in the paper
Research resources: HeLa cells RRID:CVCL_0030, HEK293FT cells RRID:CVCL_6911, Mouse: C57BL/6J RRID:IMSR_JAX:000664, MATLAB R2020b RRID:SCR_001622, Fiji/ImageJ RRID:SCR_002285, GraphPad Prism RRID:SCR_002798, RRID:SCR_007370, Python RRID:SCR_008394, RRID:SCR_013673, OriginPro (FWHM Gaussian fitting) RRID:SCR_014212, NIS-Elements AR (v5.30.00, 64-bit) RRID:SCR_014329

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repositories

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

Fakorede-Olumayowa/Temporal_Domain_Multiplexing

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: e518ada2b05e5bbab530f5c4747bbb3138749c3e, 28 November 2023
Size: 1 file
Software Heritage: not archived
Found in: the resources table
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
At the source: github.com/Fakorede-Olumayowa/Temporal_Domain_Multiplexing.git

Fakorede-Olumayowa/BAMM

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: e6819a06813123cca23ba72e21f4c7a2f90c5cb3, 18 November 2025
Languages: MATLAB (4)
Size: 15 files, 4 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
4 files
At the source: github.com/Fakorede-Olumayowa/BAMM

Zenodo 19615672

License: bsd-2-clause-netbsd
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
At the source: doi.org/10.5281/zenodo.19615672

Zenodo 19616489

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
4 files
At the source: doi.org/10.5281/zenodo.19616489

gitlab.wllsb.edu.cn/blank22/kiryl-piatkevich

License: none: the authors keep all their rights
State: unreachable at the last attempt, verified on 29 September 2026
Evidence: found in the paper
Software Heritage: not checked
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 4 checks, the latest on 29 September 2026: unreachable at the last attempt
  • 29 September 2026: unreachable at the last attempt
  • 28 September 2026: unreachable at the last attempt
  • 28 September 2026: unreachable at the last attempt
  • 28 September 2026: unreachable at the last attempt
At the source: gitlab.wllsb.edu.cn/blank22/kiryl-piatkevich/-/tree/master/Alex/Temporaldomainmultiplexing/Results

The paper's code and data availability statement is in the Data section.

Tracing map

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What the map holds:

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  • 8 scripts, each with its path and the digest of its content;
  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
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Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1016/j.crmeth.2026.101471.

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 5 keywords, 9 MeSH terms, 4 funders, 31 references, 11 RRIDs.

Cite

This paper

Fakorede, O., Rong, Z., Wang, R., Papadaki, S., Wang, X., Cao, J., Subach, F. V., Köster, R. W., Namikawa, K., & Piatkevich, K. D. (2026). Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution imaging. Cell reports methods, 6(7), 101471. https://doi.org/10.1016/j.crmeth.2026.101471

BibTeX

@article{fakorede2026development,
author = {Fakorede, Olumayowa and Rong, Zhien and Wang, Ruizhao and Papadaki, Stavrini and Wang, Xinyue and Cao, Jiayue and Subach, Fedor V and Köster, Reinhard W and Namikawa, Kazuhiko and Piatkevich, Kiryl D},
title = {{Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution imaging}},
journal = {Cell reports methods},
year = {2026},
month = may,
volume = {6},
number = {7},
pages = {101471},
publisher = {Elsevier},
issn = {2667-2375},
doi = {10.1016/j.crmeth.2026.101471},
url = {https://doi.org/10.1016/j.crmeth.2026.101471},
pmid = {42214338},
pmcid = {PMC13390083}
}

RIS

TY - JOUR
AU - Fakorede, Olumayowa
AU - Rong, Zhien
AU - Wang, Ruizhao
AU - Papadaki, Stavrini
AU - Wang, Xinyue
AU - Cao, Jiayue
AU - Subach, Fedor V
AU - Köster, Reinhard W
AU - Namikawa, Kazuhiko
AU - Piatkevich, Kiryl D
TI - Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution imaging
T2 - Cell reports methods
J2 - Cell Rep Methods
PY - 2026
DA - 2026/05/29
VL - 6
IS - 7
SP - 101471
SN - 2667-2375
PB - Elsevier
DO - 10.1016/j.crmeth.2026.101471
UR - https://doi.org/10.1016/j.crmeth.2026.101471
LA - en
ER -

CSL-JSON

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