An annotated fluorescence image dataset for training nuclear segmentation methods.

Fully-automated nuclear image segmentation is the prerequisite to ensure statistically significant, quantitative analyses of tissue preparations,applied in digital pathology or quantitative microscopy. The design of segmentation methods that work independently of the tissue type or preparation is complex, due to variations in nuclear morphology, staining intensity, cell density and nuclei aggregations. Machine learning-based segmentation methods can overcome these challenges, however high quality expert-annotated images are required for training. Currently, the limited number of annotated fluorescence image datasets publicly available do not cover a broad range of tissues and preparations. We present a comprehensive, annotated dataset including tightly aggregated nuclei of multiple tissues for the training of machine learning-based nuclear segmentation algorithms. The proposed dataset covers sample preparation methods frequently used in quantitative immunofluorescence microscopy. We demonstrate the heterogeneity of the dataset with respect to multiple parameters such as magnification, modality, signal-to-noise ratio and diagnosis. Based on a suggested split into training and test sets and additional single-nuclei expert annotations, machine learning-based image segmentation methods can be trained and evaluated.

Neuroanatomy of Hyalinella punctata: Common patterns and new characters in phylactolaemate bryozoans.

Studies on the bryozoan adult nervous system employing immunocytochemical techniques and confocal laser scanning microscopy are scarce. To gain a better view into the structure and evolution of the nervous system of the Phylactolaemata, the earliest extant branch and sister taxon to the remaining Bryozoa, this work aims to characterize the nervous system of Hyalinella punctata with immunocytochemical techniques and confocal laser scanning microscopy. The cerebral ganglion is located between the anus and the pharynx and contains a lumen. Two ganglionic horns and a circum-oral nerve ring emanate from the cerebral ganglion. The pharynx is innervated by a diffuse neural plexus with two prominent neurite bundles. The caecum is innervated by longitudinal neurite bundles and a peripheral plexus. The intestine is characterized by longitudinal and circular neurite bundles, mostly near the anus. Novel putative sensory cells were found in the foregut and intestine. The tentacle sheath is innervated by a diffuse neural plexus, which emanates from several neurite bundles from the cerebral ganglion, but also parts of the pharyngeal plexus. There are six tentacle neurite bundles of intertentacular origin. The retractor muscles are innervated by two thin neurite bundles. Several characters are described herein for the first time in Phylactolaemata: Longitudinal neurite bundles and a peripheral plexus of the caecum, putative sensory structures of the gut, retractor muscle innervation, specific duplicature band neurite bundles. The tentacle innervation differs from previous descriptions of phylactolaemates regarding the origin of the three abfrontal neurite bundles. In general, most organ systems are innervated by a diffuse plexus in phylactolaemates as opposed to gymnolaemates. In contrast to the Gymnolaemata, representatives of Phylactolaemata show a higher number of tentacle nerves. Although the plesiomorphic condition for zooidal features among bryozoans remains unclear, having a diffuse nerve plexus may represent an ancestral feature for freshwater bryozoans.