@article{GriebelSegebarthSteinetal.2023,
  author    = {Griebel, Matthias and Segebarth, Dennis and Stein, Nikolai and Schukraft, Nina and Tovote, Philip and Blum, Robert and Flath, Christoph M.},
  title     = {Deep learning-enabled segmentation of ambiguous bioimages with deepflash2},
  series = {Nature Communications},
  volume    = {14},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-023-36960-9},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-357286},
  year      = {2023},
  abstract  = {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.},
  language  = {en}
}
@article{PerniaAndradeWengerEspositoetal.2021,
  author    = {Pern{\´i}a-Andrade, Alejandro J. and Wenger, Nikolaus and Esposito, Maria S. and Tovote, Philip},
  title     = {Circuits for State-Dependent Modulation of Locomotion},
  series = {Frontiers in Human Neuroscience},
  volume    = {15},
  journal   = {Frontiers in Human Neuroscience},
  issn      = {1662-5161},
  doi       = {10.3389/fnhum.2021.745689},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249995},
  year      = {2021},
  abstract  = {Brain-wide neural circuits enable bi- and quadrupeds to express adaptive locomotor behaviors in a context- and state-dependent manner, e.g., in response to threats or rewards. These behaviors include dynamic transitions between initiation, maintenance and termination of locomotion. Advances within the last decade have revealed an intricate coordination of these individual locomotion phases by complex interaction of multiple brain circuits. This review provides an overview of the neural basis of state-dependent modulation of locomotion initiation, maintenance and termination, with a focus on insights from circuit-centered studies in rodents. The reviewed evidence indicates that a brain-wide network involving excitatory circuit elements connecting cortex, midbrain and medullary areas appears to be the common substrate for the initiation of locomotion across different higher-order states. Specific network elements within motor cortex and the mesencephalic locomotor region drive the initial postural adjustment and the initiation of locomotion. Microcircuits of the basal ganglia, by implementing action-selection computations, trigger goal-directed locomotion. The initiation of locomotion is regulated by neuromodulatory circuits residing in the basal forebrain, the hypothalamus, and medullary regions such as locus coeruleus. The maintenance of locomotion requires the interaction of an even larger neuronal network involving motor, sensory and associative cortical elements, as well as defined circuits within the superior colliculus, the cerebellum, the periaqueductal gray, the mesencephalic locomotor region and the medullary reticular formation. Finally, locomotor arrest as an important component of defensive emotional states, such as acute anxiety, is mediated via a network of survival circuits involving hypothalamus, amygdala, periaqueductal gray and medullary premotor centers. By moving beyond the organizational principle of functional brain regions, this review promotes a circuit-centered perspective of locomotor regulation by higher-order states, and emphasizes the importance of individual network elements such as cell types and projection pathways. The realization that dysfunction within smaller, identifiable circuit elements can affect the larger network function supports more mechanistic and targeted therapeutic intervention in the treatment of motor network disorders.},
  language  = {en}
}
@article{RodriguezRozadaFrantzTovote2023,
  author    = {Rodriguez-Rozada, Silvia and Frantz, Stefan and Tovote, Philip},
  title     = {Cardiac optogenetics: regulating brain states via the heart},
  series = {Signal Transduction and Targeted Therapy},
  volume    = {8},
  journal   = {Signal Transduction and Targeted Therapy},
  doi       = {10.1038/s41392-023-01582-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-357625},
  year      = {2023},
  abstract  = {No abstract available.},
  language  = {en}
}
@article{SchaeferSignoretGenestvonCollenbergetal.2020,
  author    = {Schaefer, Natascha and Signoret-Genest, J{\´e}r{\´e}my and von Collenberg, Cora R. and Wachter, Britta and Deckert, J{\"u}rgen and Tovote, Philip and Blum, Robert and Villmann, Carmen},
  title     = {Anxiety and Startle Phenotypes in Glrb Spastic and Glra1 Spasmodic Mouse Mutants},
  series = {Frontiers in Molecular Neuroscience},
  volume    = {13},
  journal   = {Frontiers in Molecular Neuroscience},
  number    = {152},
  issn      = {1662-5099},
  doi       = {10.3389/fnmol.2020.00152},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-210041},
  year      = {2020},
  abstract  = {A GWAS study recently demonstrated single nucleotide polymorphisms (SNPs) in the human GLRB gene of individuals with a prevalence for agoraphobia. GLRB encodes the glycine receptor (GlyRs) β subunit. The identified SNPs are localized within the gene flanking regions (3′ and 5′ UTRs) and intronic regions. It was suggested that these nucleotide polymorphisms modify GlyRs expression and phenotypic behavior in humans contributing to an anxiety phenotype as a mild form of hyperekplexia. Hyperekplexia is a human neuromotor disorder with massive startle phenotypes due to mutations in genes encoding GlyRs subunits. GLRA1 mutations have been more commonly observed than GLRB mutations. If an anxiety phenotype contributes to the hyperekplexia disease pattern has not been investigated yet. Here, we compared two mouse models harboring either a mutation in the murine Glra1 or Glrb gene with regard to anxiety and startle phenotypes. Homozygous spasmodic animals carrying a Glra1 point mutation (alanine 52 to serine) displayed abnormally enhanced startle responses. Moreover, spasmodic mice exhibited significant changes in fear-related behaviors (freezing, rearing and time spent on back) analyzed during the startle paradigm, even in a neutral context. Spastic mice exhibit reduced expression levels of the full-length GlyRs β subunit due to aberrant splicing of the Glrb gene. Heterozygous animals appear normal without an obvious behavioral phenotype and thus might reflect the human situation analyzed in the GWAS study on agoraphobia and startle. In contrast to spasmodic mice, heterozygous spastic animals revealed no startle phenotype in a neutral as well as a conditioning context. Other mechanisms such as a modulatory function of the GlyRs β subunit within glycinergic circuits in neuronal networks important for fear and fear-related behavior may exist. Possibly, in human additional changes in fear and fear-related circuits either due to gene-gene interactions e.g., with GLRA1 genes or epigenetic factors are necessary to create the agoraphobia and in particular the startle phenotype.},
  language  = {en}
}