Summary Fourier ptychographic microscopy (FPM) is a computational microscopy technique that enables large field of view and high-resolution microscopic imaging of biological samples. However, the FPM does not yet have an adequately capable open-source software. In order to fill this gap we are presenting novel, simple, universal, semi-automatic and highly intuitive graphical user interface (GUI) open-source application called the FPM app enabling wide-scale robust FPM reconstruction. Apart from implementing the FPM in accessible GUI app, we also made several improvements in the FPM image reconstruction process itself, making the FPM more automatic, noise-robust and faster. Availability and Implementation FPM app was implemented in MATLAB and all MATLAB codes along with standalone executable version of the FPM app and the online documentation are freely accessible at https://github.com/MRogalski96/FPM-app. Our exemplary FPM datasets may be downloaded at https://bit.ly/2MxNpGb. Supplementary information Supplementary data are available at Bioinformatics online.
Phase imaging microscopy under Gabor regime has been recently reported as an extremely simple, low cost and compact way to update a standard bright-field microscope with coherent sensing capabilities. By inserting coherent illumination in the microscope embodiment and producing a small defocus distance of the sample at the input plane, the digital sensor records an in-line Gabor hologram of the target sample, which is then numerically post-processed to finally achieve the sample’s quantitative phase information. However, the retrieved phase distribution is affected by the two well-known drawbacks when dealing with Gabor’s regime, that is, coherent noise and twin image disturbances. Here, we present a single-shot technique based on wavelength multiplexing for mitigating these two effects. A multi-illumination laser source (including 3 diode lasers) illuminates the sample and a color digital sensor (conventional RGB color camera) is used to record the wavelength-multiplexed Gabor hologram in a single exposure. The technique is completed by presenting a novel algorithm based on a modified Gerchberg–Saxton kernel to finally retrieve an enhanced quantitative phase image of the sample, enhanced in terms of coherent noise removal and twin image minimization. Experimental validations are performed in a regular Olympus BX-60 upright microscope using a 20X 0.46NA objective lens and considering static (resolution test targets) and dynamic (living spermatozoa) phase samples.
Quantitative phase microscopy (QPM) is often based on recording an object-reference interference pattern and its further phase demodulation. We propose pseudo Hilbert phase microscopy (PHPM) where we combine pseudo thermal light source illumination and Hilbert spiral transform (HST) phase demodulation to achieve hybrid hardware-software-driven noise robustness and an increase in resolution of single-shot coherent QPM. Those advantageous features stem from physically altering the laser spatial coherence and numerically restoring spectrally overlapped object spatial frequencies. The capabilities of PHPM are demonstrated by analyzing calibrated phase targets and live HeLa cells in comparison with laser illumination and phase demodulation via temporal phase shifting (TPS) and Fourier transform (FT) techniques. The performed studies verified the unique ability of PHPM to combine single-shot imaging, noise minimization, and preservation of phase details.
Fringe pattern based measurement techniques are the state-of-the-art in full-field optical metrology. They are crucial both in macroscale, e.g., fringe projection profilometry, and microscale, e.g., label-free quantitative phase microscopy. Accurate estimation of the local fringe orientation map can significantly facilitate the measurement process in various ways, e.g., fringe filtering (denoising), fringe pattern boundary padding, fringe skeletoning (contouring/following/tracking), local fringe spatial frequency (fringe period) estimation, and fringe pattern phase demodulation. Considering all of that, the accurate, robust, and preferably automatic estimation of local fringe orientation map is of high importance. In this paper we propose a novel numerical solution for local fringe orientation map estimation based on convolutional neural network and deep learning called DeepOrientation. Numerical simulations and experimental results corroborate the effectiveness of the proposed DeepOrientation comparing it with a representative of the classical approach to orientation estimation called combined plane fitting/gradient method. The example proving the effectiveness of DeepOrientation in fringe pattern analysis, which we present in this paper, is the application of DeepOrientation for guiding the phase demodulation process in Hilbert spiral transform. In particular, living HeLa cells quantitative phase imaging outcomes verify the method as an important asset in label-free microscopy.
Exposure to laser light alters cell culture examination via optical microscopic imaging techniques based on label-free coherent digital holography. To mitigate this detrimental feature, researchers tend to use a broader spectrum and lower intensity of illumination, which can decrease the quality of holographic imaging due to lower resolution and higher noise. We study the lensless digital holographic microscopy (LDHM) ability to operate in the low photon budget (LPB) regime to enable imaging of unimpaired live cells with minimized sample interaction. Low-cost off-the-shelf components are used, promoting the usability of such a straightforward approach. We show that recording data in the LPB regime (down to 7 µW of illumination power) does not limit the contrast or resolution of the hologram phase and amplitude reconstruction compared to regular illumination. The LPB generates hardware camera shot noise, however, to be effectively minimized via numerical denoising. The ability to obtain high-quality, high-resolution optical complex field reconstruction was confirmed using the USAF 1951 amplitude sample, phase resolution test target, and finally, live glial restricted progenitor cells (as a challenging strongly absorbing and scattering biomedical sample). The proposed approach based on severely limiting the photon budget in lensless holographic microscopy method can open new avenues in high-throughout (optimal resolution, large field-of-view, and high signal-to-noise-ratio single-hologram reconstruction) cell culture imaging with minimized sample interaction.
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