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Analysis of cell types is recognized as a major task in current single-cell genotyping and phenotyping. In neuroscience, 3-D neuron morphologies are often reconstructed from multi-dimensional microscopic images. Recent studies indicate that neurons could form very complicated distributions in the feature space, and thus they can be explored using manifold analysis. We have developed manifold classification toolkit software to replace the conventional clustering analysis to discover cell subtypes from three state-of-the-art collections of single neurons' 3-D morphologies that reconstructed from images. We have gathered 9208 3-D spatially registered whole mouse brain neurons from three datasets with the highest quality to date generated by the single neuron morphology community. To explore manifold distribution, our method uses minimum spanning tree-based principal skeletons to approximate locally linear embeddings, to explore the morphological feature spaces, which correspond to dendritic arbors, axonal arbors or both categories of arborization patterns of neurons. We show manifold classification is a suitable approach for a majority of often referred cell types, each of which was also discovered to contain multiple subtypes. Our results show an initial effort to employ manifold classification but not traditional clustering analysis as an alternative framework for analyzing 3-D neuron morphologies reconstructed from 3-D microscopic images. Availability and implementation Freely available at https://github.com/Mr-strlen/Cell_Pattern_Analysis_Tool.' [ABSTRACT FROM AUTHOR]

Abelson tyrosine kinase (Abl) is known to regulate axon guidance, muscle development, and cell-cell interaction in vivo. The Drosophila primary culture system offers advantages in exploring the cellular mechanisms mediated by Abl with utilizing various experimental manipulations. Here we demonstrate that single-embryo cultures exhibit stage-dependent characteristics of cellular differentiation and developmental progression in neurons and myocytes, as well as nerve-muscle contacts. In particular, muscle development critically depends on the stage of dissociated embryos. In wild-type (WT) cultures derived from embryos before stage 12, muscle cells remained within cell clusters and were rarely detected. Interestingly, abundant myocytes were spotted in Abl mutant cultures, exhibiting enhanced myocyte movement and fusion, as well as neuron-muscle contacts even in cultures dissociated from younger, stage 10 embryos. Notably, Abl myocytes frequently displayed well-expanded lamellipodia. Conversely, Abl neurons were characterized with fewer large veil-like lamellipodia, but instead had increased numbers of filopodia and darker nodes along neurites. These distinct phenotypes were equally evident in both homo- and hetero-zygous cultures (Abl/Abl vs. Abl/+) of different alleles (Abl1 and Abl4) indicating dominant mutational effects. Strikingly, in WT cultures derived from stage 10 embryos, high temperature (HT) incubation promoted muscle migration and fusion, partially mimicking the advanced muscle development typical of Abl cultures. However, HT enhanced neuronal growth with increased numbers of enlarged lamellipodia, distinct from the characteristic Abl neuronal morphology. Intriguingly, HT incubation also promoted Abl lamellipodia expansion, with a much greater effect on nerve cells than muscle. Our results suggest that Abl is an essential regulator for myocyte and neuron development and that high-temperature incubation partially mimics the faster muscle development typical of Abl cultures. Despite the extensive alterations by Abl mutations, we observed myocyte fusion events and nerve-muscle contact formation between WT and Abl cells in mixed WT and Abl cultures derived from labeled embryos. [ABSTRACT FROM AUTHOR]

Motivation Large-scale neuronal morphologies are essential to neuronal typing, connectivity characterization and brain modeling. It is widely accepted that automation is critical to the production of neuronal morphology. Despite previous survey papers about neuron tracing from light microscopy data in the last decade, thanks to the rapid development of the field, there is a need to update recent progress in a review focusing on new methods and remarkable applications. Results This review outlines neuron tracing in various scenarios with the goal to help the community understand and navigate tools and resources. We describe the status, examples and accessibility of automatic neuron tracing. We survey recent advances of the increasingly popular deep-learning enhanced methods. We highlight the semi-automatic methods for single neuron tracing of mammalian whole brains as well as the resulting datasets, each containing thousands of full neuron morphologies. Finally, we exemplify the commonly used datasets and metrics for neuron tracing bench testing. [ABSTRACT FROM AUTHOR]