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three-dimensional imaging and reconstruction of the whole ovary and testis: a new frontier for the reproductive scientist

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MOLECULAR HUMAN REPRODUCTION 2021年第3期27卷 gaab007页

作者： Fiorentino, Giulia Parrilli, Annapaola Garagna, Silvia Zuccotti, Maurizio Univ Pavia Dept Biol & Biotechnol Lazzaro Spallanzani Lab Dev Biol Via Ferrata 9 I-27100 Pavia Italy Univ Pavia Ctr Hlth Technol I-27100 Pavia Italy Swiss Fed Labs Mat Sci & Technol Ctr Xray Analyt Empa Dubendorf Switzerland

The 3D functional reconstruction of a whole organ or organism down to the single cell level and to the subcellular components and molecules is a major future scientific challenge. The recent convergence of advanced imaging techniques with an impressively increased computing power allowed early attempts to translate and combine 2D images and functional data to obtain in-silico organ 3D models. This review first describes the experimental pipeline required for organ 3D reconstruction: from the collection of 2D serial images obtained with light, confocal, light-sheet microscopy or tomography, followed by their registration, segmentation and subsequent 3D rendering. Then, we summarise the results of investigations performed so far by applying these 3D image analyses to the study of the female and male mammalian gonads. These studies highlight the importance of working towards a 3D in-silico model of the ovary and testis as a tool to gain insights into their biology during the phases of differentiation or adulthood, in normal or pathological conditions. Furthermore, the use of 3D imaging approaches opens to key technical improvements, ranging from image acquisition to optimisation and development of new processing tools, and unfolds novel possibilities for multidisciplinary research.

关键词： three-dimensional imaging volume reconstruction organ clearing confocal microscopy tomography 3D histology folliculogenesis spermatogenesis ovary testis

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Model-based iterative reconstruction for spectral-domain optical coherence tomography 26

Model-based iterative reconstruction for spectral-domain opt...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing XXVI

作者： Mason, Jonathan H. Reinwald, Yvonne Yang, Ying Waters, Sarah El Haj, Alicia Bagnaninchi, Pierre O. Univ Edinburgh MRC Ctr Regenerat Med 5 Little France Dr Edinburgh Midlothian Scotland Nottingham Trent Univ Coll Sci & Technol Dept Engn Nottingham England Keele Univ Inst Sci & Technol Med Keele Staffs England Univ Oxford Math Inst Oxford England Univ Birmingham Healthcare Technol Inst Birmingham W Midlands England

ISBN: (纸本)9781510624092

Spectral domain optical coherence tomography (OCT) offers high resolution multidimensional imaging, but generally suffers from defocussing, intensity falloff and shot noise, causing artifacts and image degradation along the imaging depth. In this work, we develop an iterative statistical reconstruction technique, based upon the interferometric synthetic aperture microscopy (ISAM) model with additive noise, to actively compensate for these effects. For the ISAM re-sampling, we use a non uniform FFT with Kaiser-Bessel interpolation, offering efficiency and high accuracy. We then employ an accelerated gradient descent based algorithm, to minimize the negative log-likelihood of the model, and include spatial or wavelet sparsity based penalty functions, to provide appropriate regularization for given image structures. We evaluate our approach with titanium oxide micro-bead and cucumber samples with a commercial spectral domain OCT system, under various subsampling regimes, and demonstrate superior image quality over traditional reconstruction and ISAM methods.

关键词： OCT ISAM demonstrate ISAM optical coherence tomography Demonstrate Spectral domain image quality image degradation

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Compressed ultrafast transmission electron microscopy: a simulation study 26

Compressed ultrafast transmission electron microscopy: a sim...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing XXVI

作者： Liu, Xianglei Zhang, Shian Yurtsever, Aycan Liang, Jinyang Inst Natl Rech Sci Ctr Energie Mat Telecommun 1650 Blvd Lionel Boulet Varennes PQ J3X 1S2 Canada East China Normal Univ State Key Lab Precis Spect 3663 North Zhongshan Rd Shanghai 200062 Peoples R China

ISBN: (纸本)9781510624092

Bringing ultrafast temporal resolution to transmission electron microscopy (TEM) has historically been challenging. Despite significant recent progress in this direction, it remains difficult to achieve sub-nanosecond temporal resolution with a single electron pulse imaging. To address this limitation, here, we propose a methodology that combines laser-assisted TEM with computational imaging methodologies based on compressed sensing (CS). In this technique, a two-dimensional (2D) transient event [i.e. (x, y) frames that vary in time] is recorded through a CS paradigm. The 2D streak image generated on a camera is used to reconstruct the datacube of the ultrafast event, with two spatial and one temporal dimensions, via a CS-based image reconstruction algorithm. Using numerical simulation, we find that the reconstructed results are in good agreement with the ground truth, which demonstrates the applicability of CS-based computational imaging methodologies to laser-assisted TEM. Our proposed method, complementing the existing ultrafast stroboscopic and nanosecond single-shot techniques, opens up the possibility for single-shot, spatiotemporal imaging of irreversible structural phenomena with sub-nanosecond temporal resolution.

关键词： Transmission electron microscopy ultrafast imaging compressed sensing streak imaging

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three-dimensional and multidimensional microscopy: image acquisition and processing XXVI

Three-Dimensional and Multidimensional Microscopy: Image Acq...

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three-dimensional and multidimensional microscopy: image acquisition and processing XXVI 2019

ISBN: (纸本)9781510624085

The proceedings contain 20 papers. The topics discussed include: fluorescence recovery after photobleaching (FRAP) with simultaneous fluorescence lifetime and time-resolved fluorescence anisotropy imaging (FLIM & tr-FAIM);evaluation of a high-speed multispectral light source for stroboscopic differential imaging for endocardial examination of daphnia magna;fast stimulated Raman projection tomography with iterative reconstruction from sparse projections;Monte Carlo model for speckle contrast imaging;model-based iterative reconstruction for spectral-domain optical coherence tomography;and feasibility study of limited-angle reconstruction based in vivo optical projection tomography.

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Signal evaluation in chromatic confocal spectral interferometry via k-space phase equality approach 26

Signal evaluation in chromatic confocal spectral interferome...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing XXVI

作者： Claus, D. Boettcher, T. Ding, L. Taphanel, M. Osten, W. Inst Lasertechnol Med & Messtech Helmholtzstr 12 D-89081 Ulm Germany Inst Tech Opt Pfaffenwaldring 9 D-70569 Stuttgart Germany Fraunhofer Inst Optron Syst Tech & Bildauswertung Fraunhoferstr 1 D-76131 Karlsruhe Germany

ISBN: (纸本)9781510624092

Chromatic confocal spectral interferometry combines the benefits of scanning free acquisition of the axial dimension with interferometrically increased depth accuracy. However, so far it has been difficult to separate the confocal signal from the interferometric signal. It is, of course, possible to apply the established CCM evaluation methods. In that case, the available phase information, that offers a decreased measurement uncertainty and to some degree the removal of disturbing artifacts at steep surface inclinations, is not taken into account. In fact, it is not straight forward to interpret the signal. In comparison to white light interference microscopy, the signal suffers from a chirp. This means that it cannot be associated with a single beating frequency, which corresponds to the interferometrically encoded z-value. However, a modified lock-in technique has in the past successfully been applied, demonstrating a significant advantage in comparison to the conventional CCM procedures. Here, we will introduce the concept of k-space phase equality, which enables the separation of the confocal and the interferometric signal and furthermore offers an extended measurement range. The principle is based on signal modification in the z-space, which corresponds to the Fourier domain of the recorded spectral signal. The evaluation is then performed in the spectral domain, where the phase signals for all z-positions with respect to the corresponding wavelength are evaluated. As a result, a phase signal with reduced aberration terms, similar to an interferometric signal, is obtained, which can hence be evaluated using established techniques.

关键词： Chromatic confocal spectral interferometry chromatic confocal microscopy confocal microscopy signal evaluation

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Non-destructive real-time monitoring of brain tumor exception by combining high-frequency ultrasounds with infrared spectroscopy 26

Non-destructive real-time monitoring of brain tumor exceptio...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing XXVI

作者： Karagiannis, Georgios Th Amanatiadis, Stamatios A. Apostolidis, Georgios K. Ormylia Fdn Art Diag Ctr GR-63071 Ormylia Chalkidiki Greece Diag Multisyst GR-63200 Nea Moudania Chalkidiki Greece

ISBN: (纸本)9781510624092

The purpose of the current paper is the development of a non-destructive imaging system for diagnostic purposes, consisting of ultrasonic transducers of high frequency and an infrared spectrometer, enabling the monitoring of the brain spatial variation and the detection of cancerous cells spreading to healthy tissues during the neurosurgical tumor exception. Ultrasound utilization during the neurosurgery, where a part of the skull is temporarily removed, is able to provide a new perspective on the imaging techniques. The proposed device combines transducers of different center frequencies in order to achieve sufficient penetration depth inside the brain and fine spatial resolution. Moreover, the infrared spectroscopy technique is utilized and combined with the ultrasound to achieve the recognition of the cancerous cells from their infrared fingerprint. The drawback of the poor penetration depth of the infrared electromagnetic waves is overcome by inserting a small diameter probe near the location of the main tumor. The probe is integrated into the same structure as the ultrasound device to receive both signals from the identical spot. Finally, advanced signal processing techniques are used to maximize separately the information of the independent systems, while the data fusion will be attempted.

关键词： ultrasonography FTIR spectroscopy gliomas phased array image fusion classification numerical simulation brain phantom

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Morphological cell image analysis for real-time monitoring of stem cell culture 26

Morphological cell image analysis for real-time monitoring o...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing XXVI

作者： Mota, Sakina Mohammed Rogers, Robert E. Haskell, Andrew W. McNeill, Eoin P. Giger, Maryellen L. Kaunas, Roland R. Gregory, Carl A. Maitland, Kristen C. Texas A&M Univ Dept Biomed Engn College Stn TX 77843 USA Texas A&M Hlth Sci Ctr Coll Med Bryan TX 77807 USA Univ Chicago Dept Radiol Chicago IL 60637 USA

ISBN: (纸本)9781510624092

The capability of mesenchymal stem cells (MSCs) to self-renew is reflected by their morphological phenotype. Cells that rapidly self-replicate (RS) are spindle-shaped and fibroblastic, while cells that slowly replicate (SR) are flattened and cuboidal. In addition to slow replication, SR cells lose most of their ability to differentiate into multiple cell lineages and promote tissue repair. Morphological evaluation can be used as a rapid screening technique to monitor culture viability in real-time and minimize the need for time consuming validation assays during expansion. We have developed an image analysis algorithm to quantitatively determine the morphological features with the goal of non-invasive and automated prediction of culture viability. The algorithm includes cell segmentation and classification. Following initial thresholding for cell localization, individual cells are segmented using region-based edge detection while clustered cells are segmented using a marker-based watershed method. In addition, classification of cell phenotype as RS or SR is accomplished using a logistic regression model. Results were validated via visual inspection from twenty individuals trained to evaluate the morphological phenotypes of MSCs. The segmentation algorithm demonstrated an accuracy of 94.03% and a mean Dice-Sorensen score of 0.71 across 15 images containing 67 cells. The classification results for the test dataset demonstrated an accuracy of 83.33%, an AUC of 0.87 +/- 0.08, and an F-measure of 0.87.

关键词： Mesenchymal stem cell morphological image analysis cell segmentation cell classification

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Hyperspectral imaging fluorescence excitation scanning (HIFEX) microscopy for live cell imaging 26

Hyperspectral imaging fluorescence excitation scanning (HIFE...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing XXVI

作者： Leavesley, Silas J. Griswold, John Robert Deal, Joshua McAlister, Kathleen Mayes, Sam Browning, Craig Parker, Marina Mayes, Samantha Gunn Rich, Thomas C. Univ S Alabama Dept Chem & Biomol Engn Mobile AL 36688 USA Univ S Alabama Dept Pharmacol Mobile AL 36688 USA Univ S Alabama Ctr Lung Biol Mobile AL 36688 USA Univ S Alabama Dept Biomed Sci Mobile AL 36688 USA Univ S Alabama Syst Engn Mobile AL 36688 USA

ISBN: (纸本)9781510624092

In the past two decades, spectral imaging technologies have expanded the capacity of fluorescence microscopy for accurate detection of multiple labels, separation of labels from cellular and tissue autofluorescence, and analysis of autofluorescence signatures. These technologies have been implemented using a range of optical techniques, such as tunable filters, diffraction gratings, prisms, interferometry, and custom Bayer filters. Each of these techniques has associated strengths and weaknesses with regard to spectral resolution, spatial resolution, temporal resolution, and signal-to-noise characteristics. We have previously shown that spectral scanning of the fluorescence excitation spectrum can provide greatly increased signal strength compared to traditional emission-scanning approaches. Here, we present results from utilizing a Hyperspectral Imaging Fluorescence Excitation Scanning (HIFEX) microscope system for live cell imaging. Live cell signaling studies were performed using HEK 293 and rat pulmonary microvascular endothelial cells (PMVECs), transfected with either a cAMP FRET reporter or a Ca2+ reporter. Cells were further labeled to visualize subcellular structures (nuclei, membrane, mitochondria, etc.). Spectral images were acquired using a custom inverted microscope (TE2000, Nikon Instruments) equipped with a 300W Xe arc lamp and tunable excitation filter (VF-5, Sutter Instrument Co., equipped with VersaChrome filters, Semrock), and run through MicroManager. Timelapse spectral images were acquired from 350-550 nm, in 5 nm increments. Spectral image data were linearly unmixed using custom MATLAB scripts. Results indicate that the HIFEX microscope system can acquire live cell image data at acquisition speeds of 8 ms/wavelength band with minimal photobleaching, sufficient for studying moderate speed cAMP and Ca2+ events.

关键词： Spectral Spectroscopy Signature Fingerprint Optical Biopsy Classification EEM

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Hyper-spectrum scanning laser optical tomography 25

Hyper-spectrum scanning laser optical tomography

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Conference on three-dimensional and multidimensional microscopy: image acquisition and processing XXV

作者： Chen, Lingling Li, Guiye Li, Yingchao Liu, Lina Liu, Ang Hu, Xuejuan Ruan, Shuangchen Shenzhen Univ Coll Optoelect Engn Shenzhen 518060 Peoples R China

ISBN: (数字)9781510614840

ISBN: (纸本)9781510614840;9781510614833

We describe a quantitative fluorescence projection tomography technique which measures the three-dimensional fluorescence spectrum in biomedical samples with size up to several millimeters. This is achieved by acquiring a series of hyperspectral images, by using laser scanning scheme, at different projection angles. We demonstrate that this technique provide a quantitative measure of the fluorescence signal by comparing the spectrum and intensity profile of a fluorescent bead phantom and also demonstrate its application to differentiating the extrinsic label and the autofluorescence in a mouse embryo.

关键词： Fluorescence microcopy three-dimensional microscopy Multi-dimensional imaging Imaging reconstruction techniques Spectrum-resolved imaging

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Single image structured illumination (SISIM) for in-vivo imaging 25

Single image structured illumination (SISIM) for in-vivo ima...

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Conference on three-dimensional and multidimensional microscopy: image acquisition and processing XXV

作者： Hoffman, Zachary R. Kivanc, Kose Di Marzio, Charles A. Northeastern Univ 360 Huntington Ave Boston MA 02115 USA Mem Sloan Kettering Canc Ctr 1275 York Ave New York NY 10021 USA

ISBN: (数字)9781510614840

ISBN: (纸本)9781510614840;9781510614833

Recently, it has been demonstrated that sectioning within a turbid media using structured illumination microscopy can be greatly enhanced through the use of a Hilbert transform algorithm. This technique, known as single image structured illumination microscopy (SISIM), provides high quality sectioning even within a strongly refracting/scattering medium, such as tissue. It is found that motion artifacts comprise a large portion of the error in in-vivo imaging. Thus, we expand on the SISIM technique by implementing an image registration algorithm which greatly mitigates motion induced artifacts. Multiple images and movies are developed to demonstrate SISIMs ability to provide real-time, in-vivo imaging of human tissue.

关键词： Structured Illumination optical sectioning thick specimen turbid media incoherent light image registration

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