## Curated Paper

Optical coherence microscopy with extended focus for in vivo embryonic imaging

Abstract:

Optical coherence microscopy (OCM) has unique advantages of high-resolution volumetric imaging without relying on exogenous labels or dyes. It combines the coherence-gated depth discrimination of optical coherence tomography (OCT) with the high lateral resolution of confocal microscopy, offering an excellent balance between the resolutions and imaging depth. However, as the lateral resolution becomes higher, the imaging depth of OCM decreases and its three-dimensional imaging capability is greatly degraded. To overcome this limitation, we used amplitude apodization to create quasi-Bessel beam illumination in order to extend the depth of focus. The lateral and axial resolutions of our OCM system were measured to be 1.6 μm and 2.9 μm in tissue. The imaging depth was extended by 3.0X (100 μm) beyond that of the standard Gaussian beam OCM. Using zebrafish embryos as a test system, we demonstrate extendedfocus OCM for structural imaging studies, which revealed the detailed anatomy deep in embryos. © (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

0.Gaussian 光束：

1.Bessel光束：

「无衍射光束」的概念是由美国Rochester大学的 J.Durnin 等人在1987年首次提出的,它是自由空间标量波动方程的一组特殊解，其场分布特点具有第一类零阶Bessel函数的表示形式。它以特殊的性质：在无界自由空间的传输过程中光强分布保持不变、中心光斑小、与传播方向垂直的各个平面上其光场分布保持相同，而且它的光强高度集中，也就是它的能量高度局域化，且不会在传播过程中遭受衍射扩散。

2.Fresnel菲涅尔透镜

Based on above:

1. Bessel 光束代替 Gaussian 光束，然而由于有限能量和维数，通常是 Quasi-Bessel 光束
2. 大多数采用轴锥棱镜，相位模板或者空间光调制器产生Quasi-Bessel 光束

To overcome this limitation, we used amplitude apodization(振幅变迹) to create quasi-Bessel beam illumination in order to extend the depth of focus.

## What can I learn from

1.这使我想起大师兄的博士论文的「基于菲涅尔透镜的SDOCT」：

2.和一篇新文章，使用 axicon lens 轴锥棱镜的SDOCT：

Extended focus depth for Fourier domain optical coherence microscopy

The Bessel beam was generated by the axicon lens and transferred to the object using a set of telescopes. The annular aperture was inserted in the first telescope to block unwanted residual rays coming from the imperfect axicon tip.

The effective spectra are deduced from Fourier transform of the interferogram using a Hamming window for apodization

4.Bessel beam in FFOCT

5.可变焦棱镜（non scanning）Fast electrically tunable lens EL-10-30-TC

## Curated Paper

Integrated Local Binary Pattern Texture Features for Classification of Breast Tissue Imaged by Optical Coherence Microscopy

Abstract:

Highlights

• Texture analysis is applied on OCM images for human breast tissue classification.

• New variants of local binary pattern (LBP) are proposed to extract texture features.

• Using multi-scale and integrated image features improves classification accuracy.

• Achieved high sensitivity (100%) and specificity (85.2%) for cancer detection.

The images utilized in our experiments in this work are en face OCM images of ex vivo human breast tissue.

Conventional spectral domain interferometry (SDI) methods suffer from the need of data linearization. When applied to optical coherence tomography (OCT), conventional SDI methods are limited in their 3D capability, as they cannot deliver direct en-face cuts. Here we introduce a novel SDI method, which eliminates these disadvantages. We denote this method as Master – Slave Interferometry (MSI), because a signal is acquired by a slave interferometer for an optical path difference (OPD) value determined by a master interferometer. The MSI method radically changes the main building block of an SDI sensor and of a spectral domain OCT set-up. The serially provided signal in conventional technology is replaced by multiple signals, a signal for each OPD point in the object investigated. This opens novel avenues in parallel sensing and in parallelization of signal processing in 3D-OCT, with applications in high-resolution medical imaging and microscopy investigation of biosamples. Eliminating the need of linearization leads to lower cost OCT systems and opens potential avenues in increasing the speed of production of en-face OCT images in comparison with conventional SDI.

## What can I learn from

1. 不稳定
2. 灵敏度不如 FDOCT
3. 成像深度浅 – 500$\mu m$

1. Bradu, A. & Podoleanu, A. G. Imaging the eye fundus with real-time en-face spectral domain optical coherence tomography. Biomed. Opt. Express 5, 1233-1249, doi:10.1364/BOE.5.001233 (2014).

## Curated Paper

Visualization and tissue classification of human breast cancer images using ultrahigh-resolution OCT

Abstract:

Breast cancer is one of the leading cause of mortality in women. Optical coherence tomography (OCT) enables three dimensional visualization of biological tissue with micrometer level resolution at high speed, and can play an important role in early diagnosis and treatment guidance of breast cancer. In this study, we imaged human breast tissue using two spectral domain OCT systems at different wavelengths: a home-built ultra-high resolution (UHR) OCT system at 840nm (measured as 2.72 µm axial and 5.52 µm lateral) and a commercial OCT system at 1300nm with standard resolution (measured as 6.5 µm axial and 15 µm lateral). We found that detailed structures of basic units found in breast tissue, such as TDLUs, ducts, adipose and fibrous stroma, can be better delineated by UHR OCT. In addition, we added phyllodes, fibrotic focus and necrotic tumor to the UHR OCT image library of breast cancer. Moreover, by using regional features derived from OCT images produced by the two systems, we developed an automated classification algorithm based on relevance vector machine (RVM) to differentiate hollow-structured adipose tissue against solid tissue. We further developed B-scan based features for RVM to classify invasive ductal carcinoma (IDC) against normal fibrous stroma tissue amongst OCT datasets produced by the two systems. With a limited number of datasets, we showed that both OCT systems can achieve a good accuracy in identifying adipose tissue. Classification in UHR OCT images achieved higher sensitivity (94%) and specificity (93%) of adipose tissue than the sensitivity (91%) and specificity (76%) in 1300 nm OCT images. In IDC classification, similarly, we achieved better results with UHR OCT images, featured an overall accuracy of 84%, sensitivity of 89% and specificity of 71% in this preliminary study. Our work may open the door towards automatic intraoperative OCT evaluation of early-stage breast cancer.

Christine Hendon的实验室，虽然她当年压根没理我的信。Basic OCT scheme：

In particular, ultra-high resolution (UHR) OCT provides images with better histological correlation.

## What can I learn from

All OCT images presented have a corresponding histology slides, which were annotated with the help of an experienced pathologist. The aspect ratio of UHR OCT images was scaled to match the dimension of the actual cross-sectional ﬁeld of view in air (3 mm by 1.78 mm), and Thorlabs OCT images were presented in their original scale.

1. Zarnescu, L. et al. Label-free characterization of vitrification-induced morphology changes in single-cell embryos with full-field optical coherence tomography. BIOMEDO 20, 096004-096004, doi:10.1117/1.JBO.20.9.096004 (2015).
2. Assayag, O. et al. Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-Clinical Study of Human Breast Tissue and Cancer Assessment. Technology in Cancer Research & Treatment 13, 455-468, doi:doi:10.7785/tcrtexpress.2013.600254 (2014).

## Curated paper

Accurate wavelength calibration method for compact CCD spectrometer

Abstract:

Wavelength calibration is an important step in charge-coupled device (CCD) spectrometers. In this paper, an accurate calibration method is proposed. A model of a line profile spectrum is built at the beginning, followed by noise reduction, bandwidth correction, and automatic peak-seeking treatment. Experimental tests are conducted on the USB4000 spectrometer with a mercury-argon calibration light source. Compared with the traditional method, the results show that this wavelength calibration procedure obtains higher accuracy and the deviations are within 0.1 nm.

1. 噪声分析与消噪算法
2. 校正带宽
3. 自动识别峰值信号

## What I can learn from

1. Woolliams, E. R., Baribeau, R., Bialek, A. & Cox, M. G. Spectrometer bandwidth correction for generalized bandpass functions. Metrologia 48, 164 (2011).

## Curated paper

Full-Field Optical Coherence Tomography as a Diagnosis Tool: Recent Progress with Multimodal Imaging

Abstract:

Full-field optical coherence tomography (FF-OCT) is a variant of OCT that is able to register 2D en face views of scattering samples at a given depth. Thanks to its superior resolution, it can quickly reveal information similar to histology without the need to physically section the sample. Sensitivity and specificity levels of diagnosis performed with FF-OCT are 80% to 95% of the equivalent histological diagnosis performances and could therefore benefit from improvement. Therefore, multimodal systems have been designed to increase the diagnostic performance of FF-OCT. In this paper, we will discuss which contrasts can be measured with such multimodal systems …

## What I can learn from

This is my goal in the near future