pull

README.md

@@ -11,17 +11,7 @@ tags:
 - image
 - animals
 - CV
-- specimen
-- imbalanced
-- interpretability
-- evolution
-- museum-images
 pretty_name: Fish-Vista
-description: >-
-  Fish images for species classification, trait identification, and trait
-  segmentation. An imbalanced specimen image dataset designed for biological and
-  evolutionary trait discovery, model interpretability, and weakly supervised
-  semantic segmentation.
 size_categories:
 - 10K<n<100K
 language:
@@ -35,26 +25,20 @@ configs:
     path: classification_test.csv
   - split: val
     path: classification_val.csv
-- config_name: trait_identification
+- config_name: species_trait_identification
   data_files:
   - split: train
     path: identification_train.csv
-  - split: in_species_test
+  - split: test_insp
     path: identification_test_insp.csv
-  - split: leave_out_species_test
+  - split: test_lvsp
     path: identification_test_lvsp.csv
-  - split: manual_annotation_test
-    path: identification_test_manual_annot.csv
   - split: val
     path: identification_val.csv
 - config_name: trait_segmentation
   data_files:
-  - split: train
-    path: segmentation_train.csv
-  - split: test
-    path: segmentation_test.csv
-  - split: val
-    path: segmentation_val.csv
+  - "segmentation_data.csv"
+  - "segmentation_masks/images/*.png"
 ---
 
 <!--
@@ -66,7 +50,7 @@ Image with caption:
 
 # Dataset Card for Fish-Visual Trait Analysis (Fish-Vista)
 * Note that the '**</Use this dataset>**' option will only load the CSV files. To download the entire dataset, including all processed images and segmentation annotations, refer to [Instructions for downloading dataset and images](https://huggingface.co/datasets/imageomics/fish-vista#instructions-for-downloading-dataset-and-images).
-* See [Example Code to Use the Segmentation Dataset](https://huggingface.co/datasets/imageomics/fish-vista#example-code-to-use-the-segmentation-dataset)
+* See [Example Code to Use the Segmentation Dataset])(https://huggingface.co/datasets/imageomics/fish-vista#example-code-to-use-the-segmentation-dataset)
 |![Figure 1](https://huggingface.co/datasets/imageomics/fish-vista/resolve/main/metadata/figures/FishVista.png)|
 |:--|
 |**Figure 1.** A schematic representation of the different tasks in Fish-Vista Dataset. |
@@ -106,8 +90,8 @@ python download_and_process_nd_images.py --save_dir Images
 ```
 /dataset/
     segmentation_masks/
+        annotations/
         images/
-        seg_id_trait_map.json
     Images/
         chunk_1
           filename 1
@@ -122,7 +106,7 @@ python download_and_process_nd_images.py --save_dir Images
         .
         .
         .
-        chunk_7
+        chunk_6
           filename 1
           filename 2
           ...
@@ -151,16 +135,16 @@ python download_and_process_nd_images.py --save_dir Images
 <!-- Add information about each of these (task, number of images per split, etc.). Perhaps reformat as <task>_<split>.csv.
 -->
 
-* **Species Classification:** `classification_<split>.csv`
+* **Species Classification (FV-419):** `classification_<split>.csv`
   * Approximately 48K images of 419 species for species classification tasks.
   * There are about 35K training, 7.6K test, and 5K validation images.
 
-* **Trait Identification:** `identification_<split>.csv`
+* **Trait Identification (FV-682):** `identification_<split>.csv`
   * 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/)).
   * About 38K training, 8K `test_insp` (species in training set), 1.9K `test_lvsp` (species not in training), and 5.2K validation images.
   * Train, test, and validation splits are generated based on traits, so there are 628 species in train, 450 species in `test_insp`, 51 species in `test_lvsp`, and 451 in the validation set (3 species only in val). 
 
-* **Trait Segmentation:** `segmentation_<split>.csv` 
+* **Trait Segmentation (FV-1200):** `segmentation_<split>.csv` 
   * Pixel-level annotations of 9 different traits for 2,427 fish images.
   * About 1.7k training, 600 test and 120 validation images for the segmentation task
   * These are also used as manually annotated test set for Trait Identification.
@@ -460,4 +444,4 @@ Kazi Sajeed Mehrab and Elizabeth G. Campolongo
 
 <!--[More Information Needed--optional]
  Could include who to contact with questions, but this is also what the "Discussions" tab is for. -->
- ksmehrab@vt.edu
+ ksmehrab@vt.edu