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README.md
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We developed 12 target classes, or trait masks, for our segmentation problem, each representing different morphological traits of a fish specimen.
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The segmentation classes are: dorsal fin, adipose fin, caudal fin, anal fin, pelvic fin, pectoral fin, head minus the eye, eye, caudal fin-ray, alt fin-ray, alt fin-spine, and trunk.
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Although minnows do not have adipose fins, the segmentation model was trained on a variety of fish image data, some of which had adipose fins.
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We retained this class because the segmentation model may erroneously assign an adipose fin to a minnow (
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The training dataset utilized the image files listed in [training_dataset_INHS.txt](https://huggingface.co/imageomics/BGNN-trait-segmentation/blob/main/training_dataset_INHS.txt).
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We developed 12 target classes, or trait masks, for our segmentation problem, each representing different morphological traits of a fish specimen.
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The segmentation classes are: dorsal fin, adipose fin, caudal fin, anal fin, pelvic fin, pectoral fin, head minus the eye, eye, caudal fin-ray, alt fin-ray, alt fin-spine, and trunk.
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Although minnows do not have adipose fins, the segmentation model was trained on a variety of fish image data, some of which had adipose fins.
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We retained this class because the segmentation model may erroneously assign an adipose fin to a minnow (Fig. S1), and a domain scientist examining these outputs may want to analyze the accuracy of the model.
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|![Figure S1](https://huggingface.co/imageomics/BGNN-trait-segmentation/raw/main/Fig_S1.png)|
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|**Figure S1.** [Image of a segmented minnow](https://huggingface.co/imageomics/BGNN-trait-segmentation/raw/main/Fig_S1.png) with an erroneously marked anal fin.
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The segmentation has 13 classes: background (black), dorsal fin (red), adipose fin (green), caudal fin (blue), anal fin (yellow), pelvic fin (light blue), pectoral fin (pink), head minus the eye (white), eye (bright green), trunk (teal), caudal fin-ray (light red), alt fin-ray (light pink), and alt fin-spine (peach).|
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The training dataset utilized the image files listed in [training_dataset_INHS.txt](https://huggingface.co/imageomics/BGNN-trait-segmentation/blob/main/training_dataset_INHS.txt).
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