Heck, Kilian Leonard (2023)
Generative Image Sequence Modeling of Optical Imaging Data.
Technische Universität Darmstadt
doi: 10.26083/tuprints-00024413
Ph.D. Thesis, Primary publication, Publisher's Version
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Item Type: | Ph.D. Thesis | ||||
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Type of entry: | Primary publication | ||||
Title: | Generative Image Sequence Modeling of Optical Imaging Data | ||||
Language: | English | ||||
Referees: | Galuske, Prof. Dr. Ralf ; Koeppl, Prof. Dr. Heinz | ||||
Date: | 11 December 2023 | ||||
Place of Publication: | Darmstadt | ||||
Collation: | xii, 140 Seiten | ||||
Date of oral examination: | 6 October 2023 | ||||
DOI: | 10.26083/tuprints-00024413 | ||||
Abstract: | This thesis focuses on the development of a data processing pipeline for inferring neural activity observed in cat's primary visual cortex. These activity patterns were measured in a grating stimulation paradigm using optical imaging based on fluorescent dyes, more specifically voltage-sensitive dye imaging. While offering a good compromise between spatial and temporal resolution, a low signal-to-noise ratio and dominant technical and biological noise components are inherent properties of the chosen data acquisition method. A high trial-to-trial variability of neural response activity poses additional challenges for data analysis. Further constraints on the chosen processing approach are presented in terms of computational efficiency as well as statistical robustness, which both are requirements for future closed-loop experimental designs. To tackle these aspects, the benefits of deep learning and probabilistic inference are taken advantage of by the utilization of a deep generative model framework, namely a variational autoencoder model architecture. Benchmarking and evaluating deep neural networks commonly requires training data with known ground truth information, which is not available for respective real data. For that purpose, an additional routine for generating synthetic image sequences resembling voltage-sensitive dye imaging recordings was developed. It incorporates knowledge about the data-generating process, including pre-defined spatio-temporal dynamics and typical signal- and artifact-related components. In six parameter studies on basis of both real and synthetic datasets, a wide range of model configurations were tested while considering different pre-processing steps. The thesis concludes with the implication that many of the tested model parametrizations offer a feasible trade-off between image reconstruction quality and model regularization, and can be adequatly used for tracking signal- and noise-related features. |
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Status: | Publisher's Version | ||||
URN: | urn:nbn:de:tuda-tuprints-244138 | ||||
Classification DDC: | 500 Science and mathematics > 570 Life sciences, biology | ||||
Divisions: | 10 Department of Biology > Systems Neurophysiology | ||||
Date Deposited: | 11 Dec 2023 13:09 | ||||
Last Modified: | 14 Feb 2024 09:45 | ||||
URI: | https://tuprints.ulb.tu-darmstadt.de/id/eprint/24413 | ||||
PPN: | 515410918 | ||||
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