Dataset for Morphological Evidence for a Directional Flow Mechanoreceptor in Olive‐Headed Sea Snakes (<i>Hydrophis major</i>)

<h2>Morphological Evidence for a Directional Flow Mechanoreceptor in Olive‐Headed Sea Snakes (<i>Hydrophis major</i>)</h2><p dir="ltr">This dataset is associated with the following publication in the Journal of Morphology: https://doi.org/10.1002/jmor.70093</p><p dir="ltr">And preprint on bioRxiv: https://doi.org/10.1101/2025.01.28.635253 </p><h2>Description of the data and file structure</h2><p dir="ltr">All data in this dataset was generated from several specimens of the sea snake <i>Hydrophis major</i>. This fully marine sea snake has one of the highest values for mechanoreceptor size, coverage and density among all snakes recorded to date, but the full distribution of mechanoreceptors over the head has not been comprehensively quantified in any sea snake. We aimed to describe mechanoreceptor morphology using scanning electron microscopy and histology, and quantitatively analyse mechanoreceptor traits (number, density, coverage, height) over the head through the novel application of gel‐based 3D profilometry (Gelsight scanner).</p><p dir="ltr">Eleven adult snakes were collected off Exmouth and Dampier, Western Australia, with approval from The University of Adelaide Animal Ethics Committee (Science) (Approval number S/2021-017) and the WA State Government (collection permit number FO25000393). Snakes were euthanised with a lethal injection of diluted pentobarbitone (60mg/mL) at a dosage of 150 mg/kg into the body cavity using a 23-30G needle. In addition to fresh fixed specimens, specimen were sourced from the South Australian Museum. Most specimens were initially frozen, then preserved in 10% formalin and stored in 70% ethanol. A subset of skin samples was taken from preserved specimens and immersed in 4% paraformaldehyde in 0.1 M phosphate buffer or Karnovsky’s solution (2% paraformaldehyde and 2.5% glutaraldehyde in 0.1 M phosphate buffer) for histology and scanning electron microscopy. Measurements of the specimen head (length, width, depth), snout to vent length and tail length were recorded using digital callipers or a tape measure.</p><p dir="ltr">This dataset is composed of four individual datasets:</p><ul><li>Scanning electron microscopy data</li><li>Histology data</li><li>Gelsight Scanner data</li><li>Snake head images</li></ul><p dir="ltr">Each dataset has its own README file detailing what data it contains and how it was generated.</p><p dir="ltr">The "Scanning electron microscopy data" contains scanning electron microscopy images of cephalic scales and associated metadata files.</p><p dir="ltr">The "Histology data" contains histology files of two cephalic scales of Hydrophis major.</p><p dir="ltr">The "Gelsight data" contains images and files generated by the Gelsight Scanner and the Software MountainsMap via analysis of the Gelsight generated files.</p><p dir="ltr">The "Snake Head Images" data contains images of the head of a specimen of Hydrophis major.</p><p dir="ltr">Data was generated by Alizée Wagner in 2024 (<a href="mailto:alizee.wagner@imbrsea.eu" target="_blank">alizee.wagner@imbrsea.eu</a>).</p><h3>Files and variables</h3><h4>File: Snake_Head_images.zip</h4><p dir="ltr"><b>Description:</b> The dataset contains .JPEG and .PPX files. they are images of the head of a male specimen of <i>Hydrophis major</i> from the South Australian Museum (Accession number R67292). The images of the specimen were taken at The University of Adelaide (Adelaide, SA, Australia) by Megan Folwell in April 2024. The images of the skin surface were manually stitched together using by multiple images output by a Gelsight 1.0X Mobile Core (GelSight Inc., Waltham, Massachusetts, USA). The powerpoint slides show how the total number of scale mechanoreceptors were identified and traced manually using the images from the Gelsight and camera. The resulting images were loaded into Fiji (Schindelin et al., 2012) to create a heatmap of mechanoreceptor density.</p><h4>File: Scanning electron microscopy data.zip</h4><p dir="ltr"><b>Description:</b> The dataset contains two types of files: images in the form of .TIF files and metadata in the form of .TXT files. The images are of cephalic skin and mechanoreceptors of three individual sea snakes (Hydrophis major). The specimens have the Field numbers KLS1502, KLS1456 and JCR0038 and were obtained from Herpetology collection of the South Australian Museum. The text file associated to each image contains metadata such as the scale, the date, the magnification and details about the instrument. The images were taken at the La Trobe bioimaging platform (Bundoora, VIC, Australia)</p><h4>File: Histology_data-20251013T045416Z-1-002.zip</h4><p dir="ltr"><b>Description</b>:The dataset contains .CZI files. They are files containing histological images of the postocular and supralabial scales of two individuals of Hydrophis major (Accession numbers KLS152 and KLS1456).</p><p dir="ltr">The samples were dehydrated in a sequential series of ethanols, sequentially embedded in Spurr's resin, placed under vacuum and then dried in an oven at 60°C. The scales were sectioned to obtain 0.75 μm cross sections using the Leica Ultramicrotome EM UC6 (Leica Microsystems Pty Ltd, Macquarie Park, NSW, Australia) fitted with a glass knife. They were then mounted on slides, stained with toluidine blue and scanned with a Zeiss Axioscan 7 slide scanner (Carl Zeiss AG, Jena, Germany) using brightfield at 20x magnification. The file format generated is .CZI, which is a format generated by Zeiss equipment to be treated in the the free software Zeiss Zen. The file has embedded metadata, which will automatically be available when the file is opened in the Zeiss Zen software. The images were taken at Adelaide Microscopy by Jane Sibbons in April 2024.</p><h4>File: Histology_data-20251013T045416Z-1-001.zip</h4><p dir="ltr"><b>Description:</b> Same info as other histology data file.</p><h4>File: Gelsight_data-20251013T053810Z-1-002.zip</h4><p dir="ltr"><b>Description:</b> The dataset contains several types of files: data tables in the form of .CSV files, images in the form of .PNG files, scanner data in the form of .TMD and .YAML files and Scale Identity sheets in the for of .PDF files. All the data regards scale mechanoreceptors of twelve individual sea snakes (Hydrophis major). The specimens have the Field and Accession numbers KLS1502, KLS1456, R67292, KLS1068, KLS1334, KLS1337, KLS1442, KLS1463, KLS1562, R174252 and JCR0038 and were obtained from Herpetology collection of the South Australian Museum. The data was generated with the GelSight Mobile Core (GelSight Inc., Waltham, Massachusetts, USA), software version 3.1.156.0. It is a non-destructive technology to capture high resolution (micron-level) surface information (5 μm and 3 mm) from any surface, including biological samples, in an area of 8.508 × 7.099 mm, using gel-based profilometry. The files were generated by Alizée Wagner (<a href="mailto:alizee.wagner@imbrsea.eu" target="_blank">alizee.wagner@imbrsea.eu</a>) between January and December 2024 (exact dates can be found in the .YAML files). The .TMD files are compatible with the software MountainsMap version 10 developed by Digital Surf. Each .TMD file is accompanied by a .YAML file providing metadata about the .TMD file (calibration, camera, software, device, generated files).</p><h4>File: Gelsight_data-20251013T053810Z-1-003.zip</h4><p dir="ltr"><b>Description:</b> Same info as other Gelsight data files.</p><h4>File: Gelsight_data-20251013T053810Z-1-001.zip</h4><p dir="ltr"><b>Description:</b> Same info as other Gelsight data files.</p><h4>File: Gelsight_data-20251013T053810Z-1-004.zip</h4><p dir="ltr"><b>Description:</b> Same info as other Gelsight data files.</p><h4>File: Gelsight_data-20251013T053810Z-1-007.zip</h4><p dir="ltr"><b>Description:</b> Same info as other Gelsight data files.</p><h4>File: Gelsight_data-20251013T053810Z-1-005.zip</h4><p dir="ltr"><b>Description:</b> Same info as other Gelsight data files.</p><h4>File: Gelsight_data-20251013T053810Z-1-006.zip</h4><p dir="ltr"><b>Description:</b> Same info as other Gelsight data files.</p><h4>File: Heatmaps script (top).ijm</h4><p dir="ltr"><b>Description:</b> Script for Fiji ImageJ to create heatmap from Snake_Head_images.zip.</p><h2>Code/software</h2><p dir="ltr">The Gelsight scanner files are .TMD and .YAML and need to be viewed in appropriate software (e.g. Matlab or Mountains Map, Digital Surf).</p><p dir="ltr">The histology data files are .CZI files and need to be viewed in Zeiss Zen software.</p><p dir="ltr">The code for creating density heatmaps is .IJM file to be run in Fiji ImageJ software.</p>