Update to reflect change to publication of subset only

README.md

@@ -10,44 +10,63 @@ tags:
 - CV
 pretty_name: Smithsonian Tropical Research Institute (STRI) Samples
 size_categories:
-- 10K<n<100K
+- n<1K
 ---
 
-# Dataset Card for STRI Samples
+# Dataset Card for Smithsonian Tropical Research Institute (STRI) Samples
 
 ## Dataset Description
 
-- **Homepage:** 
-- **Repository:** 
-- **Paper:** 
-- **Leaderboard:** 
-- **Point of Contact:** 
+- **Curated by:** Christopher Lawrence, Owen McMillan, Daniel Romero, and Carlos Arias
+<!-- Provide the basic links for the dataset. These will show up on the sidebar to the right of your dataset card ("Curated by" too). -->
+<!-- - **Homepage:** -->
+- **Repository:** https://github.com/Imageomics/wing-segmentation
+<!-- - **Paper:** -->
 
 ### Dataset Summary
 
-Images of butterfly wings collected by [Owen McMillan](https://stri.si.edu/scientist/owen-mcmillan) and members of his lab at the Smithsonian Tropical Research Institute.
+Dorsal images of butterfly wings collected by [Owen McMillan](https://stri.si.edu/scientist/owen-mcmillan) and members of his lab at the Smithsonian Tropical Research Institute.
 
-24,119 RGB images: Dorsal and Ventral images of separated wings.
+Full dataset will be 24,119 RGB images: Dorsal and Ventral images of separated wings. This sample contains 207 _dorsal_ butterfly images used as part of the training data for [Imageomics/butterfly_detection_yolo](https://huggingface.co/imageomics/butterfly_detection_yolo).
 <!---
-This dataset card aims to be a base template for new datasets. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1).
+This dataset card was generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1), and further altered to suit Imageomics Institute needs.
 --->
 
+
 ### Supported Tasks and Leaderboards
 
-[More Information Needed]
+Note that this is just a subset of a larger dataset that has yet to be curated. It was used in combination with images from other sources to train the [Imageomics/butterfly_detection_yolo](https://huggingface.co/imageomics/butterfly_detection_yolo) model, and is not large or representative enough for use in training on its own yet.
 
-### Languages
+## Dataset Structure
 
-[More Information Needed]
+<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
+
+
+```
+/dataset/
+    <images>/
+        <img_name_no_ext 1>.JPG
+        <img_name_no_ext 2>.JPG
+        ...
+        <img_name_no_ext 207>.JPG
+    metadata.csv
+```
 
-## Dataset Structure
 
 ### Data Instances
+[More Information Needed]
+
+<!--
+Describe data files
+
+Ex: All images are named <img_id>.png, each within a folder named for the species. They are 1024 x 1024, and the color has been standardized using <link to color standardization package>.
+-->
+
 
 [More Information Needed]
 
-* **Type:** JPEG and NEF
-* **Size (x pixels by y pixels):** Not yet known
+* **Type:** JPG <!-- PNG if we include the smaller images
+* **Size (x pixels by y pixels):** Not yet known (downsized are 256 x 256) -->
 * **Background (color or none):** Sometimes gray sometimes white
 * **Fit in frame:** tight
 * **Ruler or Scale:** Do not think so
@@ -55,59 +74,108 @@ This dataset card aims to be a base template for new datasets. It has been gener
 
 Potential for future addition of genetic sequencing data.
 
+There are 11 speices represented in this sample of 207. They are primarily from the genus Heliconius, but the following genera are also represented: Junonia, Eueides, Neruda, and Dryas.
+
+The CSV also includes labels regarding the quality of the specimen: `damaged`, `dorsal`, or `incomplete`, which were used for the segmentation model. Below is a species distribution chart for this data colored by quality label.
+
+![species distribution chart for STRI data colored by label](https://github.com/user-attachments/assets/92da2996-b4f0-462a-b666-4ea715669f3b)
+
 ### Data Fields
 
 [More Information Needed]
 
+Suggested columns to keep:
+
+**metadata.csv:** minimal data record for the images; this is a subset of all the information potentially available for each image since curation of this dataset is still ongoing. This also means that there are some duplicative columns (e.g., there are multiple NCSU and STRI IDs). 
+- **label:** indicates quality of specimen, either `damaged`, `dorsal`, or `incomplete`.
+- **img_name_no_ext:** `FileName` without the type extension.
+source_url, --not actually a URL. it's a box location, with the folder, seems like something to potentially remove
+source_dataset -- holdover from separating them out, can remove
+- **FileName:** filename given to image (with extension, e.g., ".JPG"). Often (??) `<NCSU_id>_D.JPG`.
+- **Folder:** folder in which images or a record is kept, seems to be date followed by number; part of the "source_url"??
+- **Box:** Box in which specimen was kept? ("Box 11" or "Box 10").
+- **Genus:** genus of the specimen; primarily "Heliconius", but also "Junonia", "Eueides", "Neruda", or "Dryas". Labeled for all images.
+- **species:** species of the specimen; 11 unique species, but mostly "erato" and "melpomene". Labeled for all but six of the images.
+- **subspecies:** subspecies of the specimen if provided, or parent subspecies if hybrid. Labeled for 168 images.
+- **subspecies II:** second parent subspecies of the specimen if it is a hybrid (there are 16 with the label "hybrid"). Labeled for 70 images.
+- **Subfamily**: subfamily of the specimen (only labeled for 18 images, all "Heliconiinae").
+- **id uncertain:** indicates uncertainty in the taxonomic identity of the specimen? -- 11 images, but there is another image with a question mark in the subspecies name.
+- **sex:** sex of the specimen ("male" or "female", one instance of "?", most labeled).
+
+MULTIPLE IDS -- keep for alignment and standardization later
+NCSU_id, ID from NCSU? Did all values have this or is it just NCSU prefix?
+NCSU #, --relation to NCSU ID and STRI ID?
+stri_id, --relation to NCSU id?
+STRI ID, -- relation to other versions above?
+Other ID,-- relation to other versions above?
+
+
+- **Date Collected:** date specimen was collected? Seem to be mostly DD-MM-YY, but not consistent.
+- **Collector:** person who collected the specimen?
+- **Taxonomic ID:** --- only labeled for 18 images, what is this? Seems to be scientific name: "Genus species (ssp x ssp II)" or "Genus species (hybrid)". Remove or do same for the remaining images?
+- **Sample type:** "Wild" or "Stocks", only labeled for 18 images.
+- **Owner of Sample:** -- only labeled for 18 images, mostly "BLUM - STRI", but also two "MCMILLAN - STRI", corresponds to Collector for BLUM, but not for MCMILLAN.
+
+
 ### Data Splits
 
-[More Information Needed]
+All of these sample images were used in training the [Imageomics/butterfly_detection_yolo](https://huggingface.co/imageomics/butterfly_detection_yolo) model.
 
 ## Dataset Creation
 
 ### Curation Rationale
 
-[More Information Needed]
+These images were selected and labeled to use in training the [Imageomics/butterfly_detection_yolo](https://huggingface.co/imageomics/butterfly_detection_yolo) model. The larger dataset is still undergoing curation.
 
 ### Source Data
 
-Images are of specimens collected by the [Smithsonian Tropical Research Institute](https://stri.si.edu/) and photographs were taken by Christopher Lawrence.
+Images are of specimens collected by the [Smithsonian Tropical Research Institute](https://stri.si.edu/) and photographs of this subset were taken by Daniel Romero.
+<!-- images taken by Christopher Lawrence have not been added yet, curation ongoing -->
 
-#### Initial Data Collection and Normalization
+#### Data Collection and Processing
+[More Information Needed]
+<!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, re-sizing of images, tools and libraries used, etc. 
+This is what _you_ did to it following collection from the original source; it will be overall processing if you collected the data initially.
+-->
 
+#### Who are the source data producers?
 [More Information Needed]
+<!-- This section describes the people or systems who originally created the data.
 
-#### Who are the source language producers?
+Ex: This dataset is a collection of images taken of the butterfly collection housed at the Ohio State University Museum of Biological Diversity. The associated labels and metadata are the information provided with the collection from biologists that study butterflies and supplied the specimens to the museum.
+ -->
 
-[More Information Needed]
 
 ### Annotations
 
 #### Annotation process
-
-[More Information Needed]
+Damage annotations were completed by Michelle Ramirez for training the [Imageomics/butterfly_detection_yolo](https://huggingface.co/imageomics/butterfly_detection_yolo) model she created.
 
 #### Who are the annotators?
-
 [More Information Needed]
+<!-- This section describes the people or systems who created the annotations. -->
 
 ### Personal and Sensitive Information
+[More Information Needed]
+<!-- 
+For instance, if your data includes people or endangered species. -->
 
-None
 
 ## Considerations for Using the Data
-
-### Social Impact of Dataset
-
 [More Information Needed]
+<!--
+Things to consider while working with the dataset. For instance, maybe there are hybrids and they are labeled in the `hybrid_stat` column, so to get a subset without hybrids, subset to all instances in the metadata file such that `hybrid_stat` is _not_ "hybrid".
+-->
 
-### Discussion of Biases
+### Bias, Risks, and Limitations
+This is a small sample of minimally curated butterfly images intended only for wing segmentation and damage detection.
 
+### Recommendations
 [More Information Needed]
+<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
 
-### Other Known Limitations
+This is not a complete dataset, nor is it curated for greater use. The purpose of this dataset is to provide the 207 image sample used as part of a larger training set for the [Imageomics/butterfly_detection_yolo](https://huggingface.co/imageomics/butterfly_detection_yolo) model. More information on the full project can be found in the [GitHub repository](https://github.com/Imageomics/wing-segmentation).
 
-[More Information Needed]
 
 ## Additional Information
 
@@ -124,8 +192,10 @@ None
 
 ### Citation Information
 
-Christopher Lawrence, Owen McMillan, Daniel Romero, Carlos Arias. (2023). Smithsonian Tropical Research Institute (STRI) Samples. Hugging Face. https://huggingface.co/datasets/imageomics/STRI-Samples.
+Christopher Lawrence, Owen McMillan, Daniel Romero, Carlos Arias. (2024). Smithsonian Tropical Research Institute (STRI) Samples. Hugging Face. https://huggingface.co/datasets/imageomics/STRI-Samples.
+
+## Acknowledgements
 
-### Contributions
+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.
 
-The [Imageomics Institute](https://imageomics.org) is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) Institute 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).
+<!-- 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. -->