Posts by Collection

Molecular Spectroscopy with the cryogenic 22-pole BerlinTrap

Published: February 15, 2018

BerlinTrap combines a cryogenic 22-pole ion trap, electrospray ion source, helium buffer gas cooling, and an orthogonal reflectron time-of-flight mass spectrometer, achieving sub-20 K temperatures. It analyzes protonated amino acids, and other protonated/metallated bio molecules, and provides UV photodissociation and visible electronic photodissociation spectra, validated by quantum chemical calculations, for precise determination of molecule structure and vibration spectra.

Enhanced Object Detection Using Random Forests and Image Augmentation Techniquess

Published: January 27, 2020

The project introduces a classical object detection pipeline for three classes, utilizing selective search for proposing regions, Histogram of Oriented Gradients (HOG) for feature extraction, random forests for window classification, and Non-Maximum Suppression (NMS) for final bounding box determination. The implementation is done in C++ using OpenCV.

3D Reconstruction from single RGB Images

Published: August 31, 2022

This work aimed to reconstruct 3D scenes from an RGB image. The pipeline adopted a two-part architecture: the first part utilized a UNet that predicted a depth map from an RGB image input, which was then voxelized into an incomplete occupancy grid. This grid was subsequently fed into the second part, IF-Net, which completed the incomplete data. The primary goal was to combine the ability to complete partial, incomplete inputs to watertight meshes, retaining both local and global details, with the capability to generate those partial inputs autonomously from RGB images. The results showcased the viability of IF-Nets for the reconstruction of large, intricate scenes. Furthermore, the project extended IF-Nets with a depth regressor and differential voxelization, enabling an end-to-end trainable 3D scene prediction network.

Neural Radiance Field Reconstruction with Depth and Normal Constraints

Published: February 15, 2023

In my master's thesis, titled "NeRF with Depth and Normal Constraints," I explored the potential of Neural Radiance Fields (NeRFs) in reconstructing 3D scenes from 2D images. The primary objective was to enhance the efficiency and accuracy of NeRFs by incorporating auxiliary image features, specifically depth and normal maps. This investigation culminated in the formulation of an innovative loss function for depth supervision. By deriving this function directly from a Gaussian likelihood of the transmittance function for a ray traversing a neural radiance field, I was able to surpass the prevailing state-of-the-art methods on widely-used datasets like ScanNet and Blender scenes. The scenes depicted herin are reconstructed from less than 20 images.

BerlinTrap: A new cryogenic 22-pole ion trap spectrometer

Published in Journal of Molecular Spectroscopy, 2017

The design and first applications of a new tandem mass spectrometer (BerlinTrap) combining an electrospray ion source, a quadrupole mass spectrometer, a cryogenic 22-pole ion trap (4–300 K), and an orthogonal reflectron time-of-flight mass spectrometer are described. The trapped ions are cooled by helium buffer gas cooling. The formation and solvation shell structure of weakly-bound He_nH₃O⁺ complexes and the electronic photodissociation spectrum of the protonated amino acid tyrosine are used to calibrate the setup for cooling, tagging, and spectroscopic capabilities. A vibrational temperature below 20 K is inferred for protonated tyrosine. The electronic spectrum of isolated protonated lumichrome, the smallest protonated flavin, is recorded in the visible range and assigned to the most stable N5 isomer by comparison with quantum chemical calculations. These results demonstrate the suitability of the BerlinTrap apparatus for spectroscopy and reactivity studies of small and large (bio-)molecular ions and their clusters.

Günther, Alan, Pablo Nieto, David Müller, Alexander Sheldrick, Dieter Gerlich, and Otto Dopfer. (2017). "BerlinTrap: A new cryogenic 22-pole ion trap spectrometer." Journal of Molecular Spectroscopy. 1(332):8-15. https://doi.org/10.1016/j.jms.2016.08.017

Optical spectroscopy of isolated flavins: photodissociation of protonated lumichrome

Published in The Royal Society of Chemistry, 2018

The optical properties of flavins strongly depend on the charge and oxidation states as well as the environment. Herein, the electronic spectrum of cold protonated lumichrome, the smallest flavin molecule, is recorded by means of photodissociation in the visible range (VISPD) in a cryogenic ion trap tandem mass spectrometer coupled to an electrospray ionization source. The vibronic spectrum is assigned to the S₁ ← S₀ (ππ*) transition of the most stable N5-protonated isomer by comparison with quantum chemical calculations at the PBE0/cc-pVDZ level in combination with multidimensional Franck–Condon simulations. Analysis of the geometric and electronic structures of neutral and protonated lumichrome explains the large red shift of the band origin upon protonation (ΔS₁ ∼ −6000 cm⁻¹), which corresponds to the increase in proton affinity upon S1 excitation as a result of charge transfer. N5 protonation greatly modifies the structure of the central pyrazine ring of the chromophore. The orbitals involved in S₁ ← S₀ excitation include an important fraction of the probability at the central ring and they are, hence, largely influenced by the positive charge of the attached proton. The rich vibronic spectrum indicates the large geometry change upon S₁ excitation. This combined experimental and computational approach is shown to be suitable to determine the optical properties of flavins as a function of oxidation, protonation, metalation, and microsolvation state.

Alexander Sheldrick, David Müller, Alan Günther, Pablo Nieto, Otto Dopfer, (2018). "Optical spectroscopy of isolated flavins: photodissociation of protonated lumichrome." The Royal Society of Chemistry. 20 (11): 7407-7414. https://doi.org/10.1039/C8CP00590G

Effect of alkali ions on optical properties of flavins: vibronic spectra of cryogenic M+lumichrome ions (M = Li–Cs) in the gas phase.

Published in Phys. Chem. Chem. Phys., 2018

The photochemical properties of flavins depend sensitively on their environment and are strongly modified by coordination with metal ions. Herein, the electronic spectra of cold complexes of the smallest flavin molecule with alkali ions are measured by photodissociation in the visible range in a cryogenic ion trap coupled to a tandem mass spectrometer and an electrospray ionization source.

Pablo Nieto, David Müller, Alexander Sheldrick, Alan Günther, Mitsuhiko Miyazaki, Otto Dopfer. (2018). Effect of alkali ions on optical properties of flavins: vibronic spectra of cryogenic M+ lumichrome ions (M= Li–Cs) in the gas phase. Phys. Chem. Chem. Phys. 2018, 20 (34): 22148-22158. http://dx.doi.org/10.1039/C8CP03950J

3D Reconstruction from single RGB-D Images

Published: September 03, 2022

The research introduces a two-part architecture for 3D reconstruction from a single RGB image. The first segment utilizes a UNet that predicts a depth map from the RGB input. This depth map is then voxelized into an incomplete occupancy grid. The second segment, IF-Net, completes this incomplete data using additional supervision from the ground truth mesh. The entire pipeline is trained end-to-end using differentiable voxelization. The study demonstrates the potential of IF-Nets for reconstructing large, intricate scenes and extends its capabilities with a depth regressor and differential voxelization.

Neural Radiance Field Reconstruction with Depth and Normal Constraints

Published: March 10, 2023

The talk for my M.Sc. thesis that addresses the problem of novel view synthesis from sparse-view supervision in the field of computer vision. Neural radiance fields (NeRFs) are a popular approach for this problem, but they rely heavily on a large dataset of images and precisely calibrated cameras. Motivated by recent advances in the area of monocular geometry prediction, which allow for cheap generation of depth- and normal maps, we systematically explore methods to incorporate these cues for the supervision of NeRFs. Our proposed method bounds the weights accumulated along rays using a Gaussian cumulative density function about the predicted depth. These bounds are directly derived from a Gaussian assumption on the likelihood of a ray being absorbed on its way through a neural volume. We show that our method, contrary to prior work, consistently improves reconstruction results for any number of training views, with photorealistic reconstructions being feasible with as few as three views. Our contribution to the field of computer vision is a flexible and easily implementable improvement to the performance of NeRFs for novel view synthesis.

Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post.

Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post.