TY  - JOUR
A1  - Griebel, Matthias
A1  - Segebarth, Dennis
A1  - Stein, Nikolai
A1  - Schukraft, Nina
A1  - Tovote, Philip
A1  - Blum, Robert
A1  - Flath, Christoph M.
T1  - Deep learning-enabled segmentation of ambiguous bioimages with deepflash2
JF  - Nature Communications
N2  - Bioimages frequently exhibit low signal-to-noise ratios due to experimental conditions, specimen characteristics, and imaging trade-offs. Reliable segmentation of such ambiguous images is difficult and laborious. Here we introduce deepflash2, a deep learning-enabled segmentation tool for bioimage analysis. The tool addresses typical challenges that may arise during the training, evaluation, and application of deep learning models on ambiguous data. The tool’s training and evaluation pipeline uses multiple expert annotations and deep model ensembles to achieve accurate results. The application pipeline supports various use-cases for expert annotations and includes a quality assurance mechanism in the form of uncertainty measures. Benchmarked against other tools, deepflash2 offers both high predictive accuracy and efficient computational resource usage. The tool is built upon established deep learning libraries and enables sharing of trained model ensembles with the research community. deepflash2 aims to simplify the integration of deep learning into bioimage analysis projects while improving accuracy and reliability.
KW  - machine learning
KW  - microscopy
KW  - quality control
KW  - software
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-357286
VL  - 14
ER  - 
TY  - JOUR
A1  - Lyutova, Radostina
A1  - Selcho, Mareike
A1  - Pfeuffer, Maximilian
A1  - Segebarth, Dennis
A1  - Habenstein, Jens
A1  - Rohwedder, Astrid
A1  - Frantzmann, Felix
A1  - Wegener, Christian
A1  - Thum, Andreas S.
A1  - Pauls, Dennis
T1  - Reward signaling in a recurrent circuit of dopaminergic neurons and peptidergic Kenyon cells
JF  - Nature Communications
N2  - Dopaminergic neurons in the brain of the Drosophila larva play a key role in mediating reward information to the mushroom bodies during appetitive olfactory learning and memory. Using optogenetic activation of Kenyon cells we provide evidence that recurrent signaling exists between Kenyon cells and dopaminergic neurons of the primary protocerebral anterior (pPAM) cluster. Optogenetic activation of Kenyon cells paired with odor stimulation is sufficient to induce appetitive memory. Simultaneous impairment of the dopaminergic pPAM neurons abolishes appetitive memory expression. Thus, we argue that dopaminergic pPAM neurons mediate reward information to the Kenyon cells, and in turn receive feedback from Kenyon cells. We further show that this feedback signaling is dependent on short neuropeptide F, but not on acetylcholine known to be important for odor-shock memories in adult flies. Our data suggest that recurrent signaling routes within the larval mushroom body circuitry may represent a mechanism subserving memory stabilization.
KW  - Learning and memory
KW  - Neural circuits
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-202161
VL  - 10
ER  -