349 research outputs found
Optimal transfer functions for bandwidth-limited imaging
No full textOne of the fundamental limits of classical optical microscopy is the diffraction limit of optical resolution. It results from the finite bandwidth of the optical transfer function (or OTF) of an optical microscope, which restricts the maximum spatial frequencies that are transmitted by a microscope. However, given the frequency support of the OTF, which is fully determined by the used optical hardware, an open and unsolved question is what is the optimal amplitude and phase distribution of spatial frequencies across this support that delivers the ``sharpest'' possible image. In this paper, we will answer this question and present a general rule how to find the optimal OTF for any given imaging system. We discuss our result in the context of optical microscopy, by considering in particular the cases of wide-field microscopy, confocal Image Scanning Microscopy (ISM), 4pi microscopy, and Structured Illumination Microscopy (SIM). Our results are important for finding optimal deconvolution algorithms for microscopy images, and we demonstrate this experimentally on the example of ISM. Our results can also serve as a guideline for designing optical systems that deliver best possible images, and they can be easily generalized to non-optical imaging such as telescopic imaging, ultrasound imaging, or magnetic resonance imaging
Optimal transfer functions for bandwidth-limited imaging
No full textOne of the fundamental limits of classical optical microscopy is the diffraction limit of optical resolution. It results from the finite bandwidth of the optical transfer function (or OTF) of an optical microscope, which restricts the maximum spatial frequencies that are transmitted by a microscope. However, given the frequency support of the OTF, which is fully determined by the used optical hardware, an open and unsolved question is what is the optimal amplitude and phase distribution of spatial frequencies across this support that delivers the ``sharpest'' possible image. In this paper, we will answer this question and present a general rule how to find the optimal OTF for any given imaging system. We discuss our result in the context of optical microscopy, by considering in particular the cases of wide-field microscopy, confocal Image Scanning Microscopy (ISM), 4pi microscopy, and Structured Illumination Microscopy (SIM). Our results are important for finding optimal deconvolution algorithms for microscopy images, and we demonstrate this experimentally on the example of ISM. Our results can also serve as a guideline for designing optical systems that deliver best possible images, and they can be easily generalized to non-optical imaging such as telescopic imaging, ultrasound imaging, or magnetic resonance imaging
Software for Simultaneous orientation and 3D localization microscopy with a Vortex point spread function
No full textThis code is distributed as accompanying software for the article Simultaneous orientation and 3D localization microscopy with a Vortex point spread function by Christiaan N. Hulleman, Rasmus Ø. Thorsen, Eugene Kim, Cees Dekker, Sjoerd Stallinga, and Bernd Rieger.Any reuse of this code should cite the original associated publication.</p
Impact of audio codec and quality on genre classificaton and BPM recognition in Essentia
No full textMusic Information Retrieval (MIR) is a field of research that focusses on extracting information from music related data. This includes the genre of music and the beats per minute (BPM) of a song. Pipelines that extract this information from music are called feature extractors. Essentia is a library for such feature extraction. Often, the audio codec and quality is not considered in research setups within the field of MIR, while this could have an influence on the results. Therefore the main research question is "How do different audio codecs and audio quality impact genre classification and beats per minute (BPM) recognition in Essentia?". To answer this, the genre has been narrowed down to rock and the chosen audio codecs are FLAC, MP3 LAME and OGG Voribs. In collaboration with Muziekweb, a Dutch music library that collects all music that has been released in The Netherlands, it was possible to gather music files in lossless format. To degrade the audio quality, classify songs and recognize BPM, python pipelines for codec conversion, rock genre classification and BPM recognition were created an ran on this data. It has been concluded that changes in audio codec and quality have an influence on genre classification and BPM recognition in Essentia. It has not been concluded which codec and quality is best to use in the field of MIR. Further research is needed to answer this.https://gitlab.ewi.tudelft.nl/cse3k-21q2-music-faithfulness/project-sjoerd-hulleman GitLab repository containing all code used for this research.CSE3000 Research ProjectComputer Science and Engineerin
Optimal transfer functions for bandwidth-limited imaging
No full textOne of the fundamental limits of classical optical microscopy is the diffraction limit of optical resolution. It results from the finite bandwidth of the optical transfer function (or OTF) of an optical microscope, which restricts the maximum spatial frequencies that are transmitted by a microscope. However, given the frequency support of the OTF, which is fully determined by the used optical hardware, an open and unsolved question is what is the optimal amplitude and phase distribution of spatial frequencies across this support that delivers the "sharpest"possible image. In this paper, we will answer this question and present a general rule how to find the optimal OTF for any given imaging system. We discuss our result in the context of optical microscopy, by considering in particular the cases of wide-field microscopy, confocal image scanning microscopy (ISM), 4pi microscopy, and structured illumination microscopy (SIM). Our results are important for finding optimal deconvolution algorithms for microscopy images, and we demonstrate this experimentally on the example of ISM. They can also serve as a guideline for designing optical systems that deliver best possible images, and can be easily generalized to nonoptical imaging such as telescopic imaging, ultrasound imaging, or magnetic resonance imaging.ImPhys/Imaging Physic
Confocal Multi-line Scanning Microscope for Efficient 3D Fluorescence Imaging
No full textConfocal fluorescent imaging is the de facto standard modality for fluorescence imaging. However, the point-to-point scanning technique leads to a very limited throughput and makes the technique unsuitable for large area and fast multi-focal scanning. We propose an architecture for highly efficient 3D line confocal fluorescence imaging. Our design extends the concept of a line scanning system with continuous ‘push broom’ scanning. Instead of using a line sensor, we use an area sensor that is tilted with respect to the optical axis to acquire image data of multiple depths simultaneously. A multi-line illumination with lines illuminating the specimen at different depths, conjugate to the tilted area sensor, is created by means of a diffractive optical element (DOE). The proposed method is suitable for fast 3D image acquisition with unlimited field of view, it requires no moving components except for the sample scanning stage, has intrinsically low losses, and provides intrinsic alignment of the simultaneously scanned layers of the focal stack.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.ImPhys/Quantitative ImagingImPhys/Imaging Physic
High-order-helix point spread functions for monocular three-dimensional imaging with superior aberration robustness
No full textAn approach for designing purely refractive optical elements that generate engineered, multi-order-helix point spread functions (PSFs) with large peak separation for passive, optical depth measurement is presented. The influence of aberrations on the PSF’s rotation angle, which limits the depth retrieval accuracy, is studied numerically and analytically. It appears that only Zernike modes with an azimuthal index that is an integer multiple of the number of PSF peaks introduce PSF rotation, and hence a depth estimation errors. This implies that high-order-helix designs have superior robustness with respect to aberrations. This is experimentally demonstrated by imaging an extended scene in the presence of severe system aberrations using novel, cost-e cient phase elements based on UV-replication on the wafer-scale.ImPhys/Imaging Physic
Accuracy of the Gaussian Point Spread Function model in 2D localization microscopy
No full textThe Gaussian function is simple and easy to implement as Point Spread Function (PSF) model for fitting the position of fluorescent emitters in localization microscopy. Despite its attractiveness the appropriateness of the Gaussian is questionable as it is not based on the laws of optics. Here we study the effect of emission dipole orientation in conjunction with optical aberrations on the localization accuracy of position estimators based on a Gaussian model PSF. Simulated image spots, calculated with all effects of high numerical aperture, interfaces between media, polarization, dipole orientation and aberrations taken into account, were fitted with a Gaussian PSF based Maximum Likelihood Estimator. For freely rotating dipole emitters it is found that the Gaussian works fine. The same, theoretically optimum, localization accuracy is found as if the true PSF were a Gaussian, even for aberrations within the usual tolerance limit of high-end optical imaging systems such as microscopes (Marechal’s diffraction limit). For emitters with a fixed dipole orientation this is not the case. Localization errors are found that reach up to 40 nm for typical system parameters and aberration levels at the diffraction limit. These are systematic errors that are independent of the total photon count in the image. The Gaussian function is therefore inappropriate, and more sophisticated PSF models are a practical necessity.Imaging Science and TechnologyApplied Science
Software related to "Impact of optical aberrations on axial position determination by photometry"
No full textSoftware distributionThis software is distributed as accompanying software for the article Impact of optical aberrations on axial position determination by photometry by Rasmus Ø. Thorsen, Christiaan N. Hulleman, Mathias Hammer, David Grünwald, Sjoerd Stallinga and Bernd Rieger.This distribution contains Matlab software to run the algorithms described in the article.MatlabThe provided scripts use Matlab (https://mathworks.com) and have been tested working in version R2017b. The scripts uses help functions from the DIPimage Toolbox and must be installed to make full use of the functions. DIPimage is a freely available image processing toolbox for Matlab (http://www.diplib.org).In the directory matlabfun all relevant Matlab functions are included. There are three examples showcasing different computations: example1.m, shows the estimated photon count for a measured bead by a fully-fledged vectorial or simplified Gaussian PSF model compared to TRABI, example2.m, computes a vectorial through-focus PSF and the corresponding photometric ratio (Gaussian fit over TRABI value) as a function of the axial position, example3.m, computes the photometric ratio over six bead measurements. These examples depict part of the data shown in the figure from the article.We hope that these examples are instructive enough to allow the interested user to apply our code. If you have any troubles please to not hesitate to contact us at the email address given below.Data availabilityAdditional data is available for download at: https://doi.org/10.4121/uuid:557b6445-5d40-402a-b214-93d7c6415195.Terms of useCopyright (C) 2018This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details (https://www.gnu.org).Quantitative Imaging GroupFaculty of Applied SciencesDelft University of TechnologyLorentzweg 1, 2628 CJ DelftThe Netherlandscontact: Bernd Rieger, [email protected]</div
Online Computational Imaging Reconstruction
No full textIn optical imaging, image quality is not only determined by the system itself but also by the media in which light traverse. Differences in the refraction index of the media encountered by a light wavefront produces phase aberrations which distort the image received from the original object. Currently, there are two main approaches for solving this problem: adaptive optics, which rely on deformable mirrors and wavefront sensors for correcting the phase aberration before it reaches the imaging sensor; and post-processing techniques, which try to estimate the object after receiving distorted images. MFBD methods are a family of algorithms that are capable of reconstructing the object by fusing the information carried by a set of differently aberrated images. These techniques are widely used in current optical systems, allowing a notable increase in image quality in most situations. However, there are cases in which they are not applicable; for example, looking at a dynamic object (e.g., a bird flying) or looking through static aberrations (e.g., in microscopy applications); but certain modifications in the optical system can be used for solving this problem.Actual optical devices have only one aperture, thus creating one full-size image on the imaging sensor but, by segmenting the pupil, several images can be retrieved at the same time with different aberrations (i.e., light follows a distinct path for each aperture). However, using a multi-aperture system implies that there is less imaging sensor area available for each aperture, thus obtaining images with less resolution. Nonetheless, MFBD algorithms can usually be extended in order to support SR, a technique that allows the increase of the object resolution by retrieving extra information from the displacement between images.This thesis is focused on the development of a functional prototype of a multi-aperture optical system that can do real-time object reconstruction. As a MFBD technique is needed, the novel TIP algorithm (developed at Delft Center for Systems and Control) is selected. In order to achieve a fast and reliable reconstruction, the algorithm is: modified for increasing its robustness against noise, expanded in order to support SR and implemented efficiently in both CPU and GPU. Finally, the system is tested in a real environment, showing promising results
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