Reviewed information on data card
Browse files
README.md
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* Approximately 48K images of 419 species for species classification tasks.
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* There are about 35K training, 7.6K test, and 5K validation images.
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* Approximately 53K images of 682 species for trait identification based on _species-level trait
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* About 38K training, 8K `test_insp` (species in training set), 1.6K `test_lvsp` (species not in training), and 5.3K validation images.
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* Train, test, and validation splits are generated based on traits, so there are 628 species in train, 471 species in `test_insp`, 51 species in `test_lvsp`, and 452 in the validation set (4 species only in val).
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* Pixel-level annotations of 9 different traits for 2,427 fish images.
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* **Image Information**
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<!-- Motivation for the creation of this dataset. For instance, what you intended to study and why that required curation of a new dataset (or if it's newly collected data and why the data was collected (intended use)), etc. -->
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Fishes are integral to both ecological systems and economic sectors, and studying fish traits is crucial for understanding biodiversity patterns and macro-evolution trends.
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Currently available fish datasets tend to focus on species classification
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The ultimate goal of Fish-Vista is to provide a clean, carefully curated, high-resolution dataset that can serve as a foundation for accelerating biological discoveries using advances in AI.
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- [Field Museum of Natural History (Zoology, FMNH) Fish Collection](https://fmipt.fieldmuseum.org/ipt/resource?r=fmnh_fishes)
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- [The Ohio State University Fish Division, Museum of Biological Diversity (OSUM), Occurrence dataset](https://doi.org/10.15468/subsl8)
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#### Data Collection and Processing
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|**Figure 4.** An overview of the data processing and filtering pipeline used to obtain Fish-Vista. |
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We carefully curated a set of
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Our pipeline incorporates rigorous stages such as duplicate removal, metadata-driven filtering, cropping, background removal using the [Segment Anything Model (SAM)](https://github.com/facebookresearch/segment-anything), and a final
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manual filtering phase. Fish-Vista supports several biologically meaningful tasks such as species
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classification, trait identification, and trait segmentation.
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#### Annotation process
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<!-- This section describes the annotation process such as annotation tools used, the amount of data annotated, annotation guidelines provided to the annotators, interannotator statistics, annotation validation, etc. -->
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[
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The annotation process for the segmentation subset was led by Wasila Dahdul. She provided guidance and oversight to a team of three people from [NEON](https://www.neonscience.org/about), who used [CVAT](https://zenodo.org/records/7863887) to label nine external traits in the images. These traits correspond to the following terms for anatomical structures in the UBERON anatomy ontology:
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1. Eye, [UBERON_0000019](http://purl.obolibrary.org/obo/UBERON_0000019)
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* Approximately 48K images of 419 species for species classification tasks.
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* There are about 35K training, 7.6K test, and 5K validation images.
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* **Trait Identification:** `identification_<split>.csv`
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* Approximately 53K images of 682 species for trait identification based on _species-level trait labels_ (i.e., presence/absence of traits based on trait labels for the species from information provided by [Phenoscape]() and [FishBase](https://www.fishbase.se/)).
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* About 38K training, 8K `test_insp` (species in training set), 1.6K `test_lvsp` (species not in training), and 5.3K validation images.
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* Train, test, and validation splits are generated based on traits, so there are 628 species in train, 471 species in `test_insp`, 51 species in `test_lvsp`, and 452 in the validation set (4 species only in val).
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* **Trait Segmentation:** `segmentation_data.csv`
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* Pixel-level annotations of 9 different traits for 2,427 fish images.
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* About x training, y test and z validation images for the segmentation task
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* These are also used as manually annotated test set for Trait Identification.
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* **Image Information**
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<!-- Motivation for the creation of this dataset. For instance, what you intended to study and why that required curation of a new dataset (or if it's newly collected data and why the data was collected (intended use)), etc. -->
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Fishes are integral to both ecological systems and economic sectors, and studying fish traits is crucial for understanding biodiversity patterns and macro-evolution trends.
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Currently available fish datasets tend to focus on species classification. They lack finer-grained labels for traits. When segmentation annotations are available in existing datasets, they tend to be for the entire specimen, allowing for segmenation of background, but not trait segmentation.
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The ultimate goal of Fish-Vista is to provide a clean, carefully curated, high-resolution dataset that can serve as a foundation for accelerating biological discoveries using advances in AI.
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- [Field Museum of Natural History (Zoology, FMNH) Fish Collection](https://fmipt.fieldmuseum.org/ipt/resource?r=fmnh_fishes)
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- [The Ohio State University Fish Division, Museum of Biological Diversity (OSUM), Occurrence dataset](https://doi.org/10.15468/subsl8)
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[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to provide the information on traits at the species level.
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[Open Tree Taxonomy](https://tree.opentreeoflife.org/) was used to standardize the species names provided by Fish-AIR.
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#### Data Collection and Processing
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|**Figure 4.** An overview of the data processing and filtering pipeline used to obtain Fish-Vista. |
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We carefully curated a set of
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60K images sourced from various museum collections through [Fish-AIR](https://fishair.org/), including [Great Lakes Invasives Network (GLIN)](https://greatlakesinvasives.org/portal/index.php), [iDigBio](https://www.idigbio.org/), and [Morphbank](https://www.morphbank.net/).
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Our pipeline incorporates rigorous stages such as duplicate removal, metadata-driven filtering, cropping, background removal using the [Segment Anything Model (SAM)](https://github.com/facebookresearch/segment-anything), and a final
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manual filtering phase. Fish-Vista supports several biologically meaningful tasks such as species
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classification, trait identification, and trait segmentation.
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#### Annotation process
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<!-- This section describes the annotation process such as annotation tools used, the amount of data annotated, annotation guidelines provided to the annotators, interannotator statistics, annotation validation, etc. -->
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[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to provide the information on species-level traits (the species-trait matrix).
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[Open Tree Taxonomy](https://tree.opentreeoflife.org/) was used to standardize the species names provided by Fish-AIR.
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Image-level trait segmentations were manually annotated as described below.
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The annotation process for the segmentation subset was led by Wasila Dahdul. She provided guidance and oversight to a team of three people from [NEON](https://www.neonscience.org/about), who used [CVAT](https://zenodo.org/records/7863887) to label nine external traits in the images. These traits correspond to the following terms for anatomical structures in the UBERON anatomy ontology:
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1. Eye, [UBERON_0000019](http://purl.obolibrary.org/obo/UBERON_0000019)
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