BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
Year: 2023
Type: article
Abstract: Whole-brain fluorescence images require several stages of computational processing to fully reveal the neuron morphology and connectivity information they contain. However, these computational tools are rarely part of an integrated pipeline. Here we present BrainLine, an open-source pipeline that interfaces with existing software to provide registration, axon segmentation, soma detection, visualization and analysis of results. By implementing a feedback based training paradigm with BrainLine, we were able to use a single learning algorithm to accurately process a diverse set of whole-brain images generated by light-sheet microscopy. BrainLine is available as part of our Python package brainlit: http://brainlit.neurodata.io/ .
Source: Neuroinformatics
Language: English
Subfield: Biophysics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,190
Awards: NeuroNex: Enabling Identification and Impact of Synaptic Weight in Functional Networks, Collaborative Research: Transferable, Hierarchical, Expressive, Optimal, Robust, Interpretable Networks, Brain networks in mouse models of aging, Biomarkers of Cognitive Decline Among Normal Individuals: The Biocard Cohort, G6671297155, Accessible technologies for high-throughput, whole-brain reconstructions of molecularly characterized mammalian neurons, DISSECTION OF THE ROLE OF SEROTONIN CIRCUITS IN REWARD AND AVERSION
OpenAlex ID: W4382893155