Computational protocol: Morphology of Dbx1 respiratory neurons in the preBötzinger complex and reticular formation of neonatal mice

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Protocol publication

[…] We visualized recorded neurons using a spinning-disk confocal microscope (Olympus BX51, Center Valley, PA) and a laser scanning confocal microscope (Zeiss LSM 510, Thornwood, NY) Three-dimensional (3D) confocal images of the individual neurons were obtained using a 20x objective (Olympus numerical aperture 0.5, Zeiss LSM numerical aperture 1.0) at increments of 1 μm in the z-axis (, step 7). The series of confocal images (i.e., z-stacks) were aligned in three-dimensions, merged or ‘stitched together’ at contiguous borders using ImageJ software and the Stitching plugin (, step 8). This stitching process was iterated until the entire morphology of the neuron was contained within a single three-dimensional image file. Finally we digitized neuronal morphologies using the Neuromantic reconstruction tool, which is also free and in the public domain. The digital reconstructions were scaled to the appropriate size based on the micron-to-pixel ratio for each microscope (, step 9). Images acquired from the LSM microscope were scaled with a 0.41 micron-to-pixel ratio and images from the Olympus microscope were scaled using a 0.322 micron-to-pixel ratio. This data descriptor pertains to 47 digital morphologies of inspiratory modulated Dbx1 preBötC neurons, six of which are previously unpublished (Data Citations 1–6) and 41 which are associated with previous publications (Data Citations 7–47). The morphologies are all publicly available via […]

Pipeline specifications

Software tools ImageJ, Stitching, Neuromantic
Databases NeuroMorpho.Org
Applications Laser scanning microscopy, Microscopic phenotype analysis
Organisms Mus musculus