DOI: 10.5061/dryad.pk0p2ngzh
title: Morphometric analysis of retinal ganglionic cells (3D confocal images) analyzed using filament tracer from Imaris software

description: This dataset contains high-resolution 3D confocal microscopy images of
 retinal ganglion cells (RGCs) from the retina of mole-rat models Fukomys
 mechowii and Fukomys anselli. The raw images were originally obtained as
 .tif files and later converted into. ims format for use with Imaris
 Software. The Imaris filament tracer extension was used to trace the
 dendritic structures of RGCs, while the soma surfaces were traced
 separately. These post-processed images are part of a study aimed at
 understanding the morphometric properties of RGCs in these mole-rat
 species and classifying them into different clusters based on their
 structural characteristics.
description: The isolated retinas of mole-rat models <em>Fukomys
 mechowii</em> and <em>Fukomys anselli</em> were spread
 flat with the retinal ganglion cell (RGC) layer facing up in a Petri dish
 with phosphate buffer at room temperature and held by a Millipore filter.
 Using an epifluorescence microscope, pre-labeled ganglion cells were
 impaled with a micropipette containing a 5% Lucifer Yellow solution, which
 was iontophoretically injected for several minutes. Up to 30 cells were
 stained in each retina. Afterward, the retina was mounted on a slide with
 glycerol and potassium iodide and imaged with a Leica confocal microscope.
 High-resolution 3D images of the RGCs were captured, and the full
 dendritic tree was traced using Imaris software's filament tracer
 tool.
description: # Morphometric analysis of retinal ganglionic cells (3D confocal images)
 analyzed using filament tracer from Imaris software
 [https://doi.org/10.5061/dryad.pk0p2ngzh](https://doi.org/10.5061/dryad.pk0p2ngzh) ## **Description of the data and file structure** **Files and variables** This dataset includes .ims files, which are compatible with Imaris Software (Version 9.2 or higher). Each file represents a 3D confocal image of Retinal Ganglion Cells (RGCs), including reconstructions of dendrites and soma. ### **File: Data\_set\_1\_morphometric\_parameters\_of\_the\_retinal\_ganglion\_cells\_analysed.xlsx** **Description:** The Excel file contains the quantitative morphometric measurements of RGCs from *Fukomys mechowii* and *Fukomys anselli*. This dataset served as the basis for all computational analyses conducted. ### **The dataset is structured as follows:** The RGCs were studied in two species of strictly subterranean rodents: the giant mole-rat (*Fukomys mechowii*) and Ansell’s mole-rat (*Fukomys anselli*). In both species, we identified five clusters of morphologically distinct RGCs. All RGCs belonging to a given cluster are grouped in the same compressed file: *Fukomys mechowii* clusters: **FMC1.zip, FMC2.zip, FMC3.zip, FMC4.zip and FMC5.zip** *Fukomys anselli* clusters: **FAC1.zip, FAC2.zip, FAC3.zip, FAC4.zip, FAC5.zip** Each compressed .rar file contains directories with data concerning individual RGCs (e.g., FM1L_Cell8, FM1L_Cell10, FM1L_Cell14). The abbreviations refer to the animal's ID (e.g., FM1), right or left retina (R or L), and cell number within that particular retina. Because of technical reasons, some cell names are more complex (e.g., FM1-22_Leye_Cell8_rb). Each RGC cluster directory contains the following files: * **(RGC_name).ims file:** A 3D skeleton of RGCs, including dendrites and soma reconstructions. These can be opened using Imaris Viewer. Select the "Filament Tracer" option and ensure the "3D Data Viewer" is enabled to view the traced dendritic structures. - **Hull folder**: 1. This folder contains .tif images providing 2D projections of the dendrites and soma separately. For example, FM1-22_Leye_Cell8_rb_hull contains the .tif images of FM1-22_Leye_Cell8_rb_DENDRITE and FM1-22_Leye_Cell8_rb_SOMA. 2. **(RGC_name) CENTROIDS.CSV:** A CSV file (e.g., FM1-22_Leye_Cell8_rb_2022-06-16T_CENTROIDS.csv) that contains measurements of centroid distances (µm), reflecting the morphological asymmetry of the dendrites relative to the soma. 3. **(RGC_name) CIRCLE.CSV**: A CSV file (e.g., FM1-22_Leye_Cell8_rb_2022-06-16T_CIRCLE.csv) that contains measurements of the total dendritic field area (µm^2). 4. **Results.CSV**: A CSV file that contains measurements of the individual 2D soma area (µm^2). - **RGC_morphometric (RGC_name).xls**: This Excel file contains individual morphometric measurements for each RGC. For example, FM1-22_Leye_Cell8_rb.xls includes data specific to dendritic branch measurements for the cell. - **RGC_morphometric_average (RGC_name_average).xls**: This Excel file contains averaged morphometric values for the dendrite structures of each RGC. For example, FM1-22_Leye_Cell8_rb_average.xls provides averaged data for all traced dendritic segments of the corresponding RGC.  ## **Code/software** **Software Requirements** * **Imaris Software**: Version 9.2 or higher (available from Bitplane). The Imaris Viewer a free version can be downloaded from the Bitplane website. * **Filament Tracer extension**: Used to generate the 3D reconstructions of the dendrites and soma. **Usage Notes** * The .ims files are compatible only with Imaris Software (Version 9.2 or higher) and require the Filament Tracer extension to fully analyze RGC dendrites and soma. The Imaris Viewer, a free version can be used to visualize the traced dendrite 3D skeleton.  * Users must have a valid license for Imaris to open and manipulate 3D/4D image data. ## **Access information** Other publicly accessible locations of the data: *  n/a Data was derived from the following sources: * **Microscope**: Leica TCS SP2 confocal microscope * **Objective**: 20x/0.7 Oil * **Pinhole**: Airy 1 * **XY Resolution**: 0.183 μm * **Z Resolution**: 1.18 μm * **Voxel Size**: 0.183 × 0.183 × 1.18 μm * **Z-stack Depth**: ~40 μm * **Excitation Laser**: 488 nm * **Emission**: 555 ± 45 nm * **Labeling**: Retinal ganglion cells were labeled with Lucifer Yellow (LY), enabling visualization of soma and dendrites.