arXiv subjects

Azeem Ahmad

Publications and source records attributed to Azeem Ahmad.

26 records · Page 2Linked to original sources

arXiv2020

A transparent waveguide chip for versatile TIRF-based microscopy and nanoscopy

Total internal reflection fluorescence microscopy (TIRF) has enabled low-background, live-cell friendly imaging of cell surfaces and other thin samples thanks to the shallow penetration of the evanescent light field into the sample. The implementation of TIRF on optical waveguide chips (c-TIRF) has overcome historical limitations on the magnification and field of view (FOV) compared to lens-based TIRF, and further allows the light to be guided in complicated patterns that can be used for advanced imaging techniques or selective stimulation of the sample. However, the opacity of the chips themselves has thus far precluded their use on inverted microscopes and complicated sample preparation and handling. In this work, we introduce a new platform for c-TIRF imaging based on a transparent substrate, which is fully compatible with sample handling and imaging procedures commonly used with a standard #1.5 glass coverslip, and is fabricated using standard complementary metal-oxide-semiconductor (CMOS) techniques, which can easily be scaled up for mass production. We demonstrate its performance on synthetic and biological samples using both upright and inverted microscopes, and show how it can be extended to super-resolution applications, achieving a resolution of 116 nm using super resolution radial fluctuations (SRRF). These new chips retain the scalable FOV of opaque chip-based TIRF and the high axial resolution of TIRF, and have the versatility to be used with many different objective lenses, microscopy methods, and handling techniques. We thus see c-TIRF as a technology primed for widespread adoption, increasing both TIRF's accessibility to users and the range of applications that can benefit from it.

physics.app-ph↗

arXiv2020

High spatially sensitive quantitative phase imaging assisted with deep neural network for classification of human spermatozoa under stressed condition

Sperm cell motility and morphology observed under the bright field microscopy are the only criteria for selecting particular sperm cell during Intracytoplasmic Sperm Injection (ICSI) procedure of Assisted Reproductive Technology (ART). Several factors such as, oxidative stress, cryopreservation, heat, smoking and alcohol consumption, are negatively associated with the quality of sperm cell and fertilization potential due to the changing of sub-cellular structures and functions which are overlooked. A bright field imaging contrast is insufficient to distinguish tiniest morphological cell features that might influence the fertilizing ability of sperm cell. We developed a partially spatially coherent digital holographic microscope (PSC-DHM) for quantitative phase imaging (QPI) in order to distinguish normal sperm cells from sperm cells under different stress conditions such as cryopreservation, exposure to hydrogen peroxide and ethanol without any labeling. Phase maps of 10,163 sperm cells (2,400 control cells, 2,750 spermatozoa after cryopreservation, 2,515 and 2,498 cells under hydrogen peroxide and ethanol respectively) are reconstructed using the data acquired from PSC-DHM system. Total of seven feedforward deep neural networks (DNN) were employed for the classification of the phase maps for normal and stress affected sperm cells. When validated against the test dataset, the DNN provided an average sensitivity, specificity and accuracy of 84.88%, 95.03% and 85%, respectively. The current approach DNN and QPI techniques of quantitative information can be applied for further improving ICSI procedure and the diagnostic efficiency for the classification of semen quality in regards to their fertilization potential and other biomedical applications in general.

physics.bio-ph↗

arXiv2019

Empirical Analysis of Factors and their Effect on Test Flakiness - Practitioners' Perceptions

Developers always wish to ensure that their latest changes to the code base do not break existing functionality. If test cases fail, they expect these failures to be connected to the submitted changes. Unfortunately, a flaky test can be the reason for a test failure. Developers spend time to relate possible test failures to the submitted changes only to find out that the cause for these failures is test flakiness. The dilemma of an identification of the real failures or flaky test failures affects developers' perceptions about what is test flakiness. Prior research on test flakiness has been limited to test smells and tools to detect test flakiness. In this paper, we have conducted a multiple case study with four different industries in Scandinavia to understand practitioners' perceptions about test flakiness and how this varies between industries. We observed that there are little differences in how the practitioners perceive test flakiness. We identified 23 factors that are perceived to affect test flakiness. These perceived factors are categorized as 1) Software test quality, 2) Software Quality, 3) Actual Flaky test and 4) Company-specific factors. We have studied the nature of effects such as whether factors increase, decrease or affect the ability to detect test flakiness. We validated our findings with different participants of the 4 companies to avoid biases. The average agreement rate of the identified factors and their effects are 86% and 86% respectively, among participants.

cs.SE↗

arXiv2019

Influence of laser spot size at diffuser plane on the longitudinal spatial coherence function of optical coherence microscopy system

Coherence properties and wavelength of light sources are indispensable for optical coherence microscopy/tomography as they greatly influence the signal to noise ratio, axial resolution, and penetration depth of the system. In the present letter, we investigated the longitudinal spatial coherence properties of the pseudo-thermal light source (PTS) as a function of spot size at the diffuser plane, which is controlled by translating microscope objective lens towards or away from the diffuser plane. The axial resolution of PTS is found to be maximum ~ 13 microns for the beam spot size of 3.5 mm at the diffuser plane. The change in the axial resolution of the system as the spot size is increased at the diffuser plane is further confirmed by performing experiments on standard gauge blocks of height difference of 15 microns. Thus, by appropriately choosing the beam spot size at the diffuser plane, any monochromatic laser light source depending on the biological window can be utilized to obtain high axial-resolution with large penetration depth and speckle-free tomographic images of multilayered biological specimens irrespective of the source temporal coherence length. In addition, PTS could be an attractive alternative light source for achieving high axial-resolution without needing chromatic aberration corrected optics and dispersion-compensation mechanism, unlike conventional setups.

physics.optics↗

arXiv2018

Highly stable common-path quantitative phase microscope for biomedical imaging

High temporal stability is the primary requirement of any quantitative phase microscope (QPM) systems for the early stage detection of various human related diseases. The high temporal stability of the system provides accurate measurement of membrane fluctuations of the biological cells, which can be good indicator of various diseases. We developed a single element highly stable common-path QPM system to obtain temporally stable holograms of the biological specimens. With the proposed system, the temporal stability is obtained ~ 15 mrad without using any vibration isolation table. The capability of the proposed system is demonstrated on USAF resolution chart, polystyrene spheres (dia. 4.5 micron) and human red blood cells (RBCs). The membrane fluctuation of healthy human RBCs is further successfully measured and found to be equal to 63 nm. Contrary to its counterparts, present system offers energy efficient, cost effective and simple way of generating object and reference beam for the development of common-path QPM.

physics.optics↗

arXiv2018

Sub-nanometer height sensitivity by phase shifting interference microscopy under ambient environmental fluctuations

Phase shifting interferometric (PSI) techniques are among the most sensitive phase measurement methods. Owing to its high sensitivity, any minute phase change caused due to environmental instability results into, inaccurate phase measurement. Consequently, a well calibrated piezo electric transducer (PZT) and highly-stable environment is mandatory for measuring accurate phase map using PSI implementation. Here, we present a new method of recording temporal phase shifted interferograms and a numerical algorithm, which can retrieve phase maps of the samples with negligible errors under the ambient environmental fluctuations. The method is implemented by recording a video of continuous temporally phase shifted interferograms and phase shifts were calculated between all the data frames using newly developed algorithm with a high accuracy less than or equal to 5.5*10-4*pi rad. To demonstrate the robustness of the proposed method, a manual translation of the stage was employed to introduce continuous temporal phase shift between data frames. The developed algorithm is first verified by performing quantitative phase imaging of optical waveguide and red blood cells using uncalibrated PZT under the influence of vibrations/air turbulence and compared with the well calibrated PZT results. Furthermore, we demonstrated the potential of the proposed approach by acquiring the quantitative phase imaging of an optical waveguide with a rib height of only 2 nm. By using 12-bit CMOS camera the height of shallow rib waveguide is measured with a height sensitivity of 4 Angstrom without using PZT and in presence of environmental fluctuations.

physics.optics↗

arXiv2018

Characterization of color cross-talk of CCD detectors and its influence in multispectral quantitative phase imaging

Multi-spectral quantitative phase imaging (QPI) is an emerging imaging modality for wavelength dependent studies of several biological and industrial specimens. Simultaneous multi-spectral QPI is generally performed with color CCD cameras. However, color CCD cameras are suffered from the color crosstalk issue, which needed to be explored. Here, we present a new approach for accurately measuring the color crosstalk of 2D area detectors, without needing prior information about camera specifications. Color crosstalk of two different cameras commonly used in QPI, single chip CCD (1-CCD) and three chip CCD (3-CCD), is systematically studied and compared using compact interference microscopy. The influence of color crosstalk on the fringe width and the visibility of the monochromatic constituents corresponding to three color channels of white light interferogram are studied both through simulations and experiments. It is observed that presence of color crosstalk changes the fringe width and visibility over the imaging field of view. This leads to an unwanted non-uniform background error in the multi-spectral phase imaging of the specimens. It is demonstrated that the color crosstalk of the detector is the key limiting factor for phase measurement accuracy of simultaneous multi-spectral QPI systems.

physics.ins-det↗

arXiv2018

Study of longitudinal coherence properties of pseudo thermal light source as a function of source size and temporal coherence

In conventional OCT, broadband light sources are generally utilized to obtain high axial resolution due to their low temporal coherence (TC) length. Purely monochromatic (i.e., high TC length) light sources like laser cannot be implemented to acquire high resolution optically sectioned images of the specimen. Contrary to this, pseudo thermal light source having high TC and low spatial coherence (SC) property can be employed to achieve high axial resolution comparable to broadband light source. In the present letter, a pseudo thermal light source is synthesized by passing a purely monochromatic laser beam through a rotating diffuser. The longitudinal coherence (LC) property of the pseudo thermal light source is studied as a function of source size and TC length. The LC length of the synthesized light source decreased as the source size increased. It is found that LC length of such light source becomes independent of the parent laser TC length for source size of greater than or equal to 3.3 mm and become almost constant at around 30 micron for both the lasers. Thus any monochromatic laser light source can be utilized to obtain high axial resolution in OCT system irrespective of its TC length. The maximum achievable axial resolution is found to be equal to 650 nm corresponding to 1.2 numerical aperture (NA) objective lens at 632 nm wavelength. The findings elucidate that pseudo thermal source being monochromatic in nature can improve the performance of existing OCT systems significantly.

physics.optics↗