Bibliography
The following publications have used AlliGator. Please consider citing one of them if you are using AlliGator in your work. Most of them are available for free on PubMed or eScholarship
Sez‐Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes, Xavier Michalet, “In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short‐lifetime near‐infrared dyes and time‐gated imaging”, Journal of Biophotonics 12 (2019) e201800185, doi:10.1002/jbio.201800185
First introduction of AlliGator (developed for this work) and demonstration of in vivo FRET analysis of time-gated data acquired with an ICCD camera. The supporting information of this article contains an extensive tutorial on phasor analysis, as well as details on data analysis with AlliGator, which can be found here. Data used in this work can be found here, here, here, here, and here.
Arin Can Ulku, Claudio Bruschini, Ivan Michel Antolovic, Yung Kuo, Rinat Ankri, Shimon Weiss, Xavier Michalet, Edoardo Charbon, “A 512 × 512 SPAD Image Sensor With Integrated Gating for Widefield FLIM”, IEEE Journal of Selected Topics in Quantum Electronics 25 (2019) 6801212, doi: 10.1109/JSTQE.2018.2867439
Use of AlliGator for time-gated decay fitting of data acquired with a custom time-gated CMOS SPAD array (with large gates). Phasor analysis presented in this article was done with a MATLAB code.
Rinat Ankri, Arkaprabha Basu, Arin Can Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Xavier Michalet, “Single-Photon, Time-Gated, Phasor-based Fluorescence Lifetime Imaging Through Highly Scattering Medium”, ACS Photonics 7 (2020) 68-79, doi: 10.1021/acsphotonics.9b00874
in vitro analysis of visible range fluorescence data acquired with SwissSPAD 2, the time-gated CMOS SPAD array introduced in [Ulku2019]. This article is associated with data than can be used to test a number of features of AlliGator.
Arin Ulku, Andrei Ardelean, Michel Antolovic, Shimon Weiss, Edoardo Charbon, Claudio Bruschini, Xavier Michalet, “Wide-field time-gated SPAD imager for phasor-based FLIM applications”, Methods and Applications in Fluorescence 8 (2020) 024002, doi: 10.1088/2050-6120/ab6ed7
More characterization of SS2 using AlliGator, as well as MATLAB code, with associated data.
Xavier Michalet, “Continuous and discrete phasor analysis of binned or time-gated periodic decays”, AIP Advances 11 (2021) 035331, doi: 10.1063/5.0027834
Used for some data illustrating this manuscript (but not central to the paper, which is concerned with theoretical considerations on phasor analysis)
Jason T Smith, Alena Rudkouskaya, Shan Gao, Juhi M Gupta, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida Barroso, Xavier Intes, Xavier Michalet, “In vitro and in vivo NIR Fluorescence Lifetime Imaging with a time-gated SPAD camera”, Optica 9 (2022) 532, doi: 10.1364/OPTICA.454790
This paper uses AlliGator for both phasor and NLSF (1-exponential and 2-exponential fits) analysis. A number of features were introduced to simplify the analysis, specifically multi-ROI, single-pixel analysis and the Fit Parameter Map, Single-exponential phasor loci (SEPL) representation, as well as significant performance improvements.
X Michalet, A Ulku, J Smith, C Bruschini, S Weiss, E Charbon, X Intes, “NIR fluorescence lifetime macroscopic imaging with a time-gated SPAD camera”, Proceedings of SPIE 11965 (2022) 1196507, doi: 10.1117/12.2607833
This proceedings paper uses AlliGator to analyze data where the gate width is larger than the laser period and demonstrates that phasor analysis works just as well in those cases.
X Michalet, A Ulku, M A Wayne, C Bruschini, S Weiss, E Charbon, “NIR fluorescence lifetime macroscopic imaging with a novel time-gated SPAD camera”, Proceedings of SPIE 12384 (2023) 1238423
This proceedings paper uses AlliGator to analyze data acquires with SwissSPAD3, which has shorter gates than the laser period and shows that phasor analysis works equally well for most cases, although the photon budget decreases for short gates.