Update README.md

README.md

@@ -156,20 +156,24 @@ English
 <!-- 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), 1.6K `test_lvsp` (species not in training), and 5.3K validation images.
-  * 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). 
+  * 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_data.csv`
+* **Trait Segmentation (FV-1200):** `segmentation_<split>.csv` 
   * Pixel-level annotations of 9 different traits for 2,427 fish images.
-  * About x training, y test and z validation images for the segmentation task
+  * 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.
 
+* **All Segmentation Data:** `segmentation_data.csv` 
+  * Essentially a collation of the trait segmentation splits
+  * Used for evaluating trait identification on the entire FV-1200
+
 
 * **Image Information**
   * **Type:** JPG
@@ -185,13 +189,12 @@ CSV Columns are as follows:
 - `source_filename`: Filename of the source image. Non-unique, since one source filename can result in multiple crops in our processed dataset.
 - `original_format`: Original format, all jpg/jpeg.
 - `arkid`: ARKID from FishAIR for the original images. Non-unique, since one source file can result in multiple crops in our processed dataset.
-- `verbatim_species`: Verbatim species label from FishAIR. This is not the name-resolved species name.
-- `species`: Scientific species name from FishAIR. This is not the name-resolved species name.
 - `family`: Taxonomic family
 - `source`: Source museum collection. GLIN, Idigbio or Morphbank
 - `owner`: Owner institution within the source collection.
 - `standardized_species`: Open-tree-taxonomy-resolved species name. This is the species name that we provide for Fish-Vista
 - `original_url`: URL to download the original, unprocessed image
+- `file_name`: Links to the image inside the repository. Necessary for HF data viewer. Not to be confused with `filename`
 - `license`: License information for the original image
 - `adipose_fin`: Presence/absence of the adipose fin trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is used for trait identification.
 - `pelvic_fin`: Presence/absence of the pelvic trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is only used for trait identification.
@@ -285,20 +288,20 @@ None
 
 ### Discussion of Biases and Other Known Limitations
 
-- This dataset is imbalanced.  
-- There are multiple images of the same specimen for many specimens; sometimes this is due to different views (eg., dorsal or ventral side)
-  - The master files contain only images that were determined to be unique (at the pixel level) through MD5 checksum.
-^This seems to be a holdover from something else--[More Information Needed]
+- This dataset is imbalanced and long tailed 
+- It inherit biased inherent to museum images
+- Train sets may contain noisy images, even if in very small numbers
+
 
 
 ### Recommendations
-[More Information Needed]
-<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
+<!--[More Information Needed]
+ This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
 
 ## Licensing Information
-[More Information Needed]
+<!--[More Information Needed]
 
-<!-- See notes at top of file about selecting a license. 
+ See notes at top of file about selecting a license. 
 If you choose CC0: This dataset is dedicated to the public domain for the benefit of scientific pursuits. We ask that you cite the dataset and journal paper using the below citations if you make use of it in your research.
 
 Be sure to note different licensing of images if they have a different license from the compilation.
@@ -357,7 +360,7 @@ Please be sure to also cite the original data sources using the citations provid
 ## Acknowledgements
 
 This work was supported by the [Imageomics Institute](https://imageomics.org), which is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
-
+We would like to thank Shelley Riders, Jerry Tatum, and Cesar Ortiz and for segmentation data annotation.
 <!-- You may also want to credit the source of your data, i.e., if you went to a museum or nature preserve to collect it. -->
 
 ## Glossary 
@@ -374,5 +377,6 @@ Kazi Sajeed Mehrab and Elizabeth G. Campolongo
 
 ## Dataset Card Contact
 
-[More Information Needed--optional]
-<!-- Could include who to contact with questions, but this is also what the "Discussions" tab is for. -->
+<!--[More Information Needed--optional]
+ Could include who to contact with questions, but this is also what the "Discussions" tab is for. -->
+ ksmehrab@vt.edu