Multispectral tracing in densely labeled mouse brain with nTracer

SUMMARY: This note describes nTracer, an ImageJ plug-in for user-guided, semi-automated tracing of multispectral fluorescent tissue samples. This approach allows for rapid and accurate reconstruction of whole cell morphology of large neuronal populations in densely labeled brains. AVAILABILITY AND IMPLEMENTATION: nTracer was written as a plug-in for the open source image processing software ImageJ. The software, instructional documentation, tutorial videos, sample image and sample tracing results are available at https://www.cai-lab.org/ntracer-tutorial. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Multispectral tracing in densely labeled mouse brain with nTracer

Summary: This note describes nTracer, an ImageJ plug-in for user-guided, semi-automated tracing of multispectral fluorescent tissue samples. This approach allows for rapid and accurate reconstruction of whole cell morphology of large neuronal populations in densely labeled brains. Availability: nTracer was written as a plugin for the open source image processing software ImageJ. The software, instructional documentation, tutorial videos, sample image and sample tracing results are available at https://www.cai-lab.org/ntracer-tutorial. Supplementary information: Supplementary data are available at Bioinformatics online

Exploring Neuronal Heterogeneity in the Drosophila Nervous System with Novel Neurotechnologies

The complex nervous system is built upon a vastly heterogeneous population of neurons. In order to decipher how the nervous system operates, it is critical to understand all aspects of neuronal properties such as morphology, lineage, electrophysiology and molecular identity, etc. Canonical neuronal subtype classification is often based on features reflected in one of these attributes. However, canonically defined neuronal subtypes normally compose of individuals that are heterogeneous in other attributes. It is therefore important to study the same neuron based on a collective cohort of properties. In this thesis study, I studied the lineage composition, morphology patterning and molecular heterogeneity of the serotonergic neurons in the fruit fly Drosophila melanogaster. I developed a series of novel transgenic tools, collectively called Bitbow, which are capable of generating up to tens of thousands of unique fluorescent barcodes to unambiguously label hundreds of lineages or individual neurons in the same brain. My results indicated that most of the serotonergic neurons arises from distinct lineages. Combining with Expansion Microscopy and multispectral neuronal tracing, a morphological map of serotonergic neurons in the ventral nerve cord was reconstructed from a single Bitbow fly. Using scRNAseq techniques, I found profound molecular heterogeneity of serotonergic neurons, characterized by their differentially expressed genes of GPCRs, ion channels, neurotransmitters, transcription factors and so on. My thesis has provided new methodologies to better define neuronal subtypes with multiple modalities, and accumulated knowledge to allow more precise investigations and manipulations of Drosophila serotonergic neurons in future studies.PHDCell and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/153346/1/cnliye_1.pd