DOI: 10.5061/dryad.j3tx95xs2
title: Segmentations of 3D electron microscopy image volume from an albino mouse dorsal lateral geniculate nucleus

description: In albino mice and EphB1 knock out mice, mistargeted retinal ganglion cell
 (RGC) axons form dense islands of axon terminals in the dorsal lateral
 geniculate nuclei (dLGN). The formation of these islands of retinal input
 depends on developmental patterns of spontaneous retinal activity. We
 reconstructed the microcircuitry of the activity-dependent islands and
 found that the boundaries of the island represent a remarkably strong
 segregation within retinogeniculate connectivity. We conclude that, when
 sets of retinal input are established in the wrong part of the dLGN, the
 developing circuitry responds by forming a synaptically isolated
 subcircuit within the otherwise fully connected network. The fact that
 there is a developmental starting condition that can induce a synaptically
 segregated microcircuit has important implications for our understanding
 of the organization of visual circuits and for our understanding of the
 implementation of activity-dependent development.
description: Serial section electron microscopy was used to image a region of
 the dorsal lateral geniculate nucleus of an adult albino mouse. Images
 were collected with a 20 nm pixel size and 40 nm section thickness. Cells
 were reconstructed manually in VAST and rendered using CellNav
 (https://github.com/MorganLabShare/albinoIsland2025, doi:
 10.5281/zenodo.14968598).
description: # Segmentations of 3D electron microscopy image volume from an albino
 mouse dorsal lateral geniculate nucleus
 [https://doi.org/10.5061/dryad.j3tx95xs2](https://doi.org/10.5061/dryad.j3tx95xs2) **Description of the data and file structure** The KxS dataset is a serial section electron microscopy reconstruction of the albino mouse dorsal lateral geniculate nucleus (dLGN). This dataset was acquired to test the hypothesis that mistargeted retinal ganglion cells form a segregated retinogeniculate circuit in the albino dLGN. The dataset consists of 40nm thick ultrathin sections imaged at 20nm pixel size. The analysis of this data set is presented in : McCracken S, McCoy L, Hu Z, Hodges J, Valkova K, Williams PR, Morgan J. Mistargeted retinal axons induce a synaptically independent subcircuit in the visual thalamus of albino mice. bioRxiv [Preprint]. 2024 Dec 3:2024.07.15.603571. doi: 10.1101/2024.07.15.603571. PMID: 39071408; PMCID: PMC11275878. The best way to access the data is to download the CellNav Matlab package from GitHub (https://github.com/MorganLabShare/albinoIsland2025, doi: 10.5281/zenodo.14968598). The CellNav viewer can then be used to display cells by type or ID number. **Files and variables** **File: CellNav_KxS_light.zip** The zip file contains the folder structure and files that can be read by CellNav. CellNav is a Matlab software package developed by Josh L. Morgan to analyze 3D electron microscopy reconstructions of neural circuits. All displays and analysis of the KxS dataset that were published in “Mistargeted retinal axons induce a synaptically independent subcircuit in the visual thalamus of albino mice.” can be reproduced using the KxS_light cell library. To access the data, unzip the download file and save the CellNav_KxS folder. When you run CellNav, it will ask you to identify the location of the CellNav_KxS folder. The data used in the publication is in the volume labeled “FullVolume” **CellNav Library folder structure** The main CellNav Folder reflects the ability of segmentations from multiple image volumes to be integrated into a single segmentation library. Information specific to individual image volumes is stored in the CellNav/Volumes folder. Information from volumes can be merged into a “Main” volume. This information will be stored in CellNav/Analysis. CellNav/saves stores images and movies generated by CellNav renderings. For the KxS dataset, all published data is stored in the v1 volume that can be found in KxS_cellNav/Volumes/FullVolume. The FullVolume volume includes the fvLibrary of segmenations merged as one 3D mesh for each cell. The fvObjects library includes a 3D mesh for each segmentation object generated in VAST. Tis.mat is a matlab structure containing information about the dataset derived from segmentations. **Code/software** CellNav is a package of Matlab code that is used by the Morgan lab to analyze neural circuit reconstructions. The package centers around a gui that can import manual segmentations of EM data from VAST and display surface meshes. Project specific analysis code is integrated into CellNav. The version of CellNav used to process KxS is available at (https://github.com/MorganLabShare/albinoIsland2025, doi: 10.5281/zenodo.14968598).