DOI: 10.5281/zenodo.8233379
title: Data from: A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics

description: Data and results from the Imageomics Workflow. These include data files from the Fish-AIR repository (https://fishair.org/) for purposes of reproducibility and outputs from the application-specific imageomics workflow contained in the Minnow_Segmented_Traits repository (https://github.com/hdr-bgnn/Minnow_Segmented_Traits).


Fish-AIR:
This is the dataset downloaded from Fish-AIR, filtering for Cyprinidae and the Great Lakes Invasive Network (GLIN) from the Illinois Natural History Survey (INHS) dataset. These files contain information about fish images, fish image quality, and path for downloading the images. The data download ARK ID is dtspz368c00q. (2023-04-05). The following files are unaltered from the Fish-AIR download. We use the following files:


extendedImageMetadata.csv: A CSV file containing information about each image file. It has the following columns: ARKID, fileNameAsDelivered, format, createDate, metadataDate, size, width, height, license, publisher, ownerInstitutionCode. Column definitions are defined https://fishair.org/vocabulary.html and the persistent column identifiers are in the meta.xml file.


imageQualityMetadata.csv: A CSV file containing information about the quality of each image. It has the following columns: ARKID, license, publisher, ownerInstitutionCode, createDate, metadataDate, specimenQuantity, containsScaleBar, containsLabel, accessionNumberValidity, containsBarcode, containsColorBar, nonSpecimenObjects, partsOverlapping, specimenAngle, specimenView, specimenCurved, partsMissing, allPartsVisible, partsFolded, brightness, 
uniformBackground, onFocus, colorIssue, quality, resourceCreationTechnique. Column definitions are defined https://fishair.org/vocabulary.html and the persistent column identifiers are in the meta.xml file.


multimedia.csv: A CSV file containing information about image downloads. It has the following columns: ARKID, parentARKID, accessURI, createDate, modifyDate, fileNameAsDelivered, format, scientificName, genus, family, batchARKID, batchName, license, source, ownerInstitutionCode. Column definitions are defined https://fishair.org/vocabulary.html and the persistent column identifiers are in the meta.xml file.


meta.xml: A XML file with the metadata about the column indices and URIs for each file contained in the original downloaded zip file. This file is used in the fish-air.R script to extract the indices for column headers.


The outputs from the Minnow_Segmented_Traits workflow are:


sampling.df.seg.csv: Table with tallies of the sampling of image data per species during the data cleaning and data analysis. This is used in Table S1 in Balk et al. 


presence.absence.matrix.csv: The Presence-Absence matrix from segmentation, not cleaned. This is the result of the combined outputs from the presence.json files created by the rule “create_morphological_analysis”. The cleaned version of this matrix is shown as Table S3 in Balk et al.


heatmap.avg.blob.png and heatmap.sd.blob.png: Heatmaps of average area of biggest blob per trait (heatmap.avg.blob.png) and standard deviation of area of biggest blob per trait (heatmap.sd.blob.png). These images are also in Figure S3 of Balk et al.


minnow.filtered.from.iqm.csv: Filtered fish image data set after filtering (see methods in Balk et al. for filter categories).


burress.minnow.sp.filtered.from.iqm.csv: Fish image data set after filtering and selecting species from Burress et al. 2017.
description: All information needed to run this workflow and generate these files can be found on the readme file on Minnow_Segemented_Traits.