This Cottle_readme20230823.txt file was generated on 20230823 by Brian Cottle. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: "Dataset for: Anatomical Variations of the Cardiac Conduction System in Healthy Neonatal Human Hearts" 2. Author Information Principal Investigator Contact Information Name: Robert Hitchcock Institution: University of Utah Address: Sorenson Molecular Biotechnology Building, Room 409 36 S Wasatch Drive Salt Lake City, UT 84112 Email: r.hitchcock@utah.edu Associate or Co-investigator Contact Information Name: Frank Sachse Institution: University of Utah Address: The Nora Eccles Harrison CVRTI 95 S 2000 E, Room 204A Salt Lake City, UT 84112-5000 Email: frank.sachse@utah.edu Associate or Co-investigator Contact Information Name: Brian Cottle Institution: University of Utah Address: The Nora Eccles Harrison CVRTI 95 S 2000 E, Room 204A Salt Lake City, UT 84112-5000 Email: brian.cottle@utah.edu 3. Date of data collection 20210401 - 20230831 4. Geographic location of data collection (where was data collected?): Salt Lake City, Utah 5. Information about funding sources that supported the collection of the data: These data were generated with help funding sources: NIH-R01 HL135077 NSF-GRFP 2139322 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC BY NC - Allows others to use and share your data non-commercially and with attribution. 2. Links to publications that cite or use the data: Cottle, B., Schriewer, K., Tiwari, S., Sachse, F., Miller, D., Kaza, A., Hitchcock, R. 2023. Anatomical Variations of the Cardiac Conduction System in Healthy Neonatal Human Hearts, Scientific Reports, 2023 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: The complete dataset can be downloaded at the following link: https://downloads.lib.utah.edu/hive.utah.edu/AnatomicalVariationsOfTheCardiacConductionSystemInHealthyNeonatalHumanHearts.zip Dataset checksum (SHA-512) https://downloads.lib.utah.edu/hive.utah.edu/AnatomicalVariationsOfTheCardiacConductionSystemInHealthyNeonatalHumanHearts.txt 5. Was data derived from another source? No 6. Recommended citation for the data: Cottle, B., Schriewer, K., Tiwari, S., Sachse, F., Miller, D., Kaza, A., Hitchcock, R. 2023. Anatomical Variations of the Cardiac Conduction System in Healthy Neonatal Human Hearts, The Hive: University of Utah Research Data Repository, https://doi.org/10.7278/S50d-a5t5-5jm8. --------------------- DATA & FILE OVERVIEW --------------------- 1. File structure and list Within the root folder of the dataset, there are 19 sub-folders, each with a name consisting of a heart-id followed by an underscore and a sample-id. For example: - 01_02 - 05_01 - 15_02 The heart-id is a unique identifier arbitrarily given to each heart as they arrived from our provider. Some heart-id numbers were skipped because those samples did not contain the correct amount or region of tissue for use in our study. Hence, the samples included here were the only ones that had sufficient tissue in the correct regions for inclusion in the study. The sample-id indicates whether the tissue sample was from the sinus or AV nodal regions in the heart. Sinus = "01", and AV = "02", since the sinus node comes first in the electrical progression of the heart. Each sample folder contains the following files/folder: - sample_name_reference_images.tif (i.e. 01_02_reference_images.tif) - This file is a tif image stack that contains processed and registered images in sequence of the serial tissue sections included in the analysis. The easiest and least complicated method for opening this file is to use FIJI (or ImageJ) to open the image. Simply drag the image over to the FIJI console and drop it in the window to initial loading and opening the file for viewing. - sample_name_segmentation_visualization.tif (i.e. 01_02_segmentation_visualization.tif) - This file is a tif image stack that contains the processed, registered, images with segmentation overlays to visualize the results of our segmentation network. Best practice for viewing this image stack follows the same protocol as the reference_images.tif stack. - sample_name_video.mp4 - This file is an mp4 video of a view of the 3D rendering of the model created for this analysis. The video rotates 360 degrees around each model. - JPG (folder) - This folder contains the serial jpg images of the histological tissue sections used in this study. Each image follows the naming format of sample_name_section_number.jpg (i.e. 01_02_55.jpg). The section_number is the number in the sequence of sections taken from the tissue. Some numbers are missing from the sequence; these images were images that didn't meet quality standards (excessive tearing, unusable staining/imaging, etc). 2. Relationship between files: Described above. 3. Additional related data collected that was not included in the current data package: N/A 4. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Tissue samples (roughly 1cm^3 in size) were gathered that included the sinus and AV nodal regions from donor pediatric human hearts. These tissue samples were sectioned (approximately 25µm between sections) in their entirety. These tissue sections were then imaged using an automated slide scanner. The resulting images were processed, registered, and segmented using a deep segmentation network (U-Net). These segmentations were then stacked to create 3D volumes for each segmentation (neural, nodal, vascular, etc), and from these volumes the subsequent visualizations were created that are included in this dataset. The code for producing the results from this paper can be found at the following GitHub repositories: 1. https://github.com/brian-cottle/Histology-ML - This repository contains the python code necessary for creating the dataset for and training the computer vision segmentation model for the study. 2. https://github.com/brian-cottle/pediatric-heart-models - This repository contains the MATLAB code necessary to perform the classical image processing for the 2D and 3D image generation, registration, and visualization. 2. Methods for processing the data: N/A 3. Instrument- or software-specific information needed to interpret the data: FIJI, or ImageJ, located at https://imagej.net/software/fiji/downloads 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: N/A 6. Describe any quality-assurance procedures performed on the data: N/A 7. People involved with sample collection, processing, analysis and/or submission: B. Cottle ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [FILENAME] ----------------------------------------- 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List A. Name: [variable name] Description: [description of the variable] Value labels if appropriate N/A B. Name: [variable name] Description: [description of the variable] Value labels if appropriate N/A 4. Missing data codes: Code/symbol Definition Code/symbol Definition N/A 5. Specialized formats of other abbreviations used N/A