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AyediOmar edited this page Mar 22, 2022 · 1 revision

OCT-A ANALYSIS by AYEDI Omar, MD

I. General description:

  • OCT-A ANALYSIS is a macro that automates operations in ImageJ used to analyze OCT-A angiograms.
  • This program is especially useful for case series studies. It automates the analysis of OCT-A.
  • ==>Accelerate data collection
  • ==>Improve the reproducibility of results
  • The program is currently intended to process grayscale angiograms with a resolution of 320*320pixels. Otherwise the measurements of the FAZ will be erroneous.
  • Other resolutions will be supported in the next update.

II. Files needed: 1. Imagej software

  • Link: https://imagej.nih.gov/ij/download.html

  • NB: The ImageJ software is directly executable, no installation required. Just download the file and unzip it. 2. The macro + 3 plugins

  • Link: https://mega.nz/folder/Gk0l0CgK#2BBm3JJqhuJWFfBmtUDRrg

  • OCT-A ANALYSIS.ijm (version 1.0.0)

  • FeatureJ_.jar (version 2.0.0)

  • imagescience.jar (version 3.0.0)

  • MorphoLibJ_-1.4.0.jar (version 1. 4.0)

  • These plugins must be installed in the ImageJ software by copying the files to ..\ImageJ\plugins (See video).

  • The macro must be installed from the ImageJ software using the command: Plugins > Macros > Install (See video).

III. Tutorial

  • Import the grayscale angiogram
  • Select the size of the field of vision: 33mm, 4.54.5mm, 66mm or 99mm
  • Manually trace the central avascular zone  The program automatically measures the following parameters: Area, Perimeter and Circularity of the FAZ
  • The program measures the intensity of the signal in the FAZ which can be considered as noise ==> In the measurement of vascular densities you have the choice to take this parameter into consideration to control it (cancel the noise differences between the acquisitions /patients).
  • The vascular densities are measured at the level of the EXTTRAFOVEAL microcirculation:
  • o Vascular density without any filter or thresholding
  • o Vascular skeleton density without any filter or thresholding
  • o Vascular density after thresholding by the “Mean” method
  • o Vascular density after thresholding by the “Huang” method
  • o Vascular density after Hessian filter + double thresholding (Multilevel: “Mean” + “Huang”)
  • o Vascular skeleton density after Hessian filter + double thresholding (Multilevel: “Mean” + “Huang”) + skeletonization

  • All measured vascular densities represent the area of the white pixels reported to the area of the angiogram after EXCLUSION of the FAZ  The results will be independent of the size of the FAZ

  • For each angiogram processed, an OUTPUT folder is created at the location of the image and contains:

  • o FAZoutline: angiogram with plotted FAZ and area, perimeter and circularity values
  • o VAD Without Threshold: binarized angiogram without thresholding
  • o VSD Without Threshold: binarized and skeletonized angiogram without thresholding
  • o VAD Huang: binarized angiogram + Huang thresholding
  • o VAD Mean: binarized angiogram + Mean thresholding
  • o VAD Multilevel: binarized angiogram + Multilevel thresholding
  • o VSD Multilevel: binarized + skeletonized angiogram + Multilevel thresholding
  • o FAZ biomarkers: Excel file containing the results of the FAZ
  • o PERFUSION biomarkers: Excel file containing vascular density measurements
  • o FAZ.roi: a memory of the manual tracing in order to have it on hand when you need it (prospective study 😉)
  • Tutorial video: In the downloaded folder.

IV. Bibliographic references on “image processing”

1. Quantification and Noise Reduction:

  • Kim, Alice Y., Zhongdi Chu, Anoush Shahidzadeh, Ruikang K. Wang, Carmen A. Puliafito, et Amir H. Kashani. « Quantifying Microvascular Density and Morphology in Diabetic Retinopathy Using Spectral-Domain Optical Coherence Tomography Angiography ». Investigative Ophthalmology & Visual Science 57, no 9 (01 2016): OCT362-370. https://doi.org/10.1167/iovs.15-18904.
  • Nesper, Peter L., Philipp K. Roberts, Alex C. Onishi, Haitao Chai, Lei Liu, Lee M. Jampol, et Amani A. Fawzi. « Quantifying Microvascular Abnormalities With Increasing Severity of Diabetic Retinopathy Using Optical Coherence Tomography Angiography ». Investigative Opthalmology & Visual Science 58, no 6 (23 octobre 2017): BIO307. https://doi.org/10.1167/iovs.17-21787.

2. Multilevel Thresholding

  • Uji A, Balasubramanian S, Lei J,Baghdasary an E, Al-Sheikh M, Sadda SR. Impact ofMultiple En Face Image Averaging on QuantitativeAssessme ntfrom Optical Coherence Tomography Angiography Images. Ophthalmology. 2017; 124(7):944–52. https://doi.org/10.1016/j.ophtha.2017.02.006 PMID: 28318637.
  • Rabiolo, Alessandro, Francesco Gelormini, Riccardo Sacconi, Maria Vittoria Cicinelli, Giacinto Triolo, Paolo Bettin, Kouros Nouri-Mahdavi, Francesco Bandello, et Giuseppe Querques. « Comparison of Methods to Quantify Macular and Peripapillary Vessel Density in Optical Coherence Tomography Angiography ». PloS One 13, no 10 (2018): e0205773. https://doi.org/10.1371/journal.pone.0205773.

3. Thresholding Methods: OTSU, MEAN, MEDIAN, MULTILEVEL ….

  • Rabiolo, Alessandro, Francesco Gelormini, Riccardo Sacconi, Maria Vittoria Cicinelli, Giacinto Triolo, Paolo Bettin, Kouros Nouri-Mahdavi, Francesco Bandello, et Giuseppe Querques. « Comparison of Methods to Quantify Macular and Peripapillary Vessel Density in Optical Coherence Tomography Angiography ». PloS One 13, no 10 (2018): e0205773. https://doi.org/10.1371/journal.pone.0205773.

4. Others (image processing)

  • Al-Sheikh, Mayss, Nopasak Phasukkijwatana, Rosa Dolz-Marco, Mansour Rahimi, Nicholas A. Iafe, K. Bailey Freund, SriniVas R. Sadda, et David Sarraf. « Quantitative OCT Angiography of the Retinal Microvasculature and the Choriocapillaris in Myopic Eyes ». Investigative Ophthalmology & Visual Science 58, no 4 (1 avril 2017): 2063 69. https://doi.org/10.1167/iovs.16-21289.
  • Ashraf, Mohammed, Peter L. Nesper, Lee M. Jampol, Fei Yu, et Amani A. Fawzi. « Statistical Model of Optical Coherence Tomography Angiography Parameters That Correlate With Severity of Diabetic Retinopathy ». Investigative Ophthalmology & Visual Science 59, no 10 (01 2018): 4292 98. https://doi.org/10.1167/iovs.18-24142.

5. Reproducibility of manual FAZ measurements

  • Zhao Q, Yang WL, Wang XN, Wang RK, You QS, Chu ZD, et al. Repeatability and Reproducibility of Quantitative Assessment of the Retinal Microvasculature Using Optical Coherence Tomography Angiography Based on Optical Microangiography. Biomed Environ Sci BES. juin 2018;31(6):407‑12.
  • Guo J, She X, Liu X, Sun X. Repeatability and Reproducibility of Foveal Avascular Zone Area Measurements Using AngioPlex Spectral Domain Optical Coherence Tomography Angiography in Healthy Subjects. Ophthalmol J Int Ophtalmol Int J Ophthalmol Z Augenheilkd. 2017;237(1):21‑8.
  • Shahlaee A, Pefkianaki M, Hsu J, Ho AC. Measurement of Foveal Avascular Zone Dimensions and its Reliability in Healthy Eyes Using Optical Coherence Tomography Angiography. Am J Ophthalmol. janv 2016;161:50-55.e1.
  • Mastropasqua R, Toto L, Mattei PA, Di Nicola M, Zecca IAL, Carpineto P, et al. Reproducibility and repeatability of foveal avascular zone area measurements using swept-source optical coherence tomography angiography in healthy subjects. Eur J Ophthalmol. 11 mai 2017;27(3):336‑41.

6. Reproducibility of vascular density measurements by ImageJ

  • Mastropasqua R, Toto L, Mastropasqua A, Aloia R, De Nicola C, Mattei PA, et al. Foveal avascular zone area and parafoveal vessel density measurements in different stages of diabetic retinopathy by optical coherence tomography angiography. Int J Ophthalmol. 2017;10(10):1545‑51.
  • Lei J, Durbin MK, Shi Y, Uji A, Balasubramanian S, Baghdasaryan E, et al. Repeatability and Reproducibility of Superficial Macular Retinal Vessel Density Measurements Using Optical Coherence Tomography Angiography En Face Images. JAMA Ophthalmol. 01 2017;135(10):1092‑8.
  • Al-Sheikh M, Tepelus TC, Nazikyan T, Sadda SR. Repeatability of automated vessel density measurements using optical coherence tomography angiography. Br J Ophthalmol. 1 avr 2017;101(4):449‑52.
  • You Q, Freeman WR, Weinreb RN, Zangwill L, Manalastas PIC, Saunders LJ, et al. Reproducibility Of Vessel Density Measurement With Optical Coherence Tomography Angiography In Eyes With And Without Retinopathy. Retina Phila Pa. août 2017;37(8):1475‑82.

V. Coming soon

  • Support for different resolutions
  • Automatic tracing of the FAZ
  • Other FAZ biomarkers : FAZ axis
  • Other perfusion biomarkers: extrafoveal avascular area, lacunarity/fractal dimension
  • Choriocapillaris analysis: flow density, fractal dimension, flow voids (count, total area, %area..)

VI. Contact: ayedi.omar@outlook.com

  • For any suggestion
  • For script modifications so it suits to your study/methodology
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