DFG Collaborative Research Center 1404 at Humboldt-Universität zu Berlin
B2: Portable and Adaptive Data Analysis Workflows for Real-Time 3D Vision
Description
Within this project, we plan to establish an abstract description of common components of 3D vision data analysis workflows (DAWs) that allows for an efficient distribution on different computing hardware infrastructure as well as a simple adaptation to different experimental settings and sensors. The work includes the analysis, modularization and optimization of DAWs and vision algorithms with respect to computational and memory demands, scalability, data dependencies, and adaptability. The focus will initially be on three specific types of 3D vision / 3D reconstruction DAWs in the area of microscopy with visible light and high-energy electrons that are very diverse in their use of memory and data transfer rate, and suitable schemes of parallelization, namely optical reflection tomography of fossils captured in amber on a microscopic scale, 3D atomic-resolution electron ptychography in the transmission electron microscope, and real time tracking of microscopic FIB lamellae within a focused ion beam instrument.
@article{schloz2022high,
title = {High Resolution Three-Dimensional Reconstructions in Electron Microscopy Through Multifocus Ptychography},
author = {Marcel Schloz and Thomas C Pekin and Hamish G Brown and Jim Ciston and Christoph T Koch},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Microscopy and Microanalysis},
volume = {28},
number = {S1},
pages = {364--366},
publisher = {Cambridge University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hamish G Brown; Philipp M Pelz; Shang-Lin Hsu; Zimeng Zhang; Ramamoorthy Ramesh; Katherine Inzani; Evan Sheridan; Sinéad M Griffin; Marcel Schloz; Thomas C Pekin; others
A three-dimensional reconstruction algorithm for scanning transmission electron microscopy data from a single sample orientation Journal Article
In: Microscopy and Microanalysis, vol. 28, no. 5, pp. 1632–1640, 2022.
@article{brown2022three,
title = {A three-dimensional reconstruction algorithm for scanning transmission electron microscopy data from a single sample orientation},
author = {Hamish G Brown and Philipp M Pelz and Shang-Lin Hsu and Zimeng Zhang and Ramamoorthy Ramesh and Katherine Inzani and Evan Sheridan and Sinéad M Griffin and Marcel Schloz and Thomas C Pekin and others},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Microscopy and Microanalysis},
volume = {28},
number = {5},
pages = {1632--1640},
publisher = {Cambridge University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{pekin2022approaches,
title = {Approaches Taken to Streamline and Consolidate Large Dataset Processing Techniques, with a Focus on Ptychography},
author = {Thomas C Pekin and Marcel Schloz and Pablo Fernandez Robledo and Anton Gladyshev and Sherjeel Shabih and Benedikt Haas and Christoph T Koch},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Microscopy and Microanalysis},
volume = {28},
number = {S1},
pages = {2994--2996},
publisher = {Cambridge University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{schloz2022deep,
title = {Deep Reinforcement Learning for Data-Driven Adaptive Scanning in Ptychography},
author = {Marcel Schloz and Johannes Müller and Thomas C Pekin and Wouter Van den Broek and Christoph T Koch},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {arXiv preprint arXiv:2203.15413},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{gladyshev2022lossy,
title = {Lossy Compression of Electron Diffraction Patterns for Ptychography via Change of Basis},
author = {Anton Gladyshev and Thomas C Pekin and Marcel Schloz and Benedikt Haas and Johannes Müller and Christoph T Koch},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {arXiv preprint arXiv:2211.07372},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
