Individual beetle images (#25)

- Upload folder using huggingface_hub (1d7a9d395697998d3f789b44e357278398fc2327)
- uploaded manually cropped individual specimen images (100759b7235eaf35a658f0a1f65e6df432a6aca6)
- updated README from individualID to pictureID (77d8b72e8f8021d8e197ddbe6c4d1121e804f13f)
- added individual_specimens to to the config of README (eb7cb4ae5614f92f6ac45e2bdac9fd99262aedef)


Co-authored-by: Mridul Khurana <[email protected]>

README.md

@@ -32,6 +32,11 @@ configs:
   data_files:
   - "beetle_images_resized/metadata.csv"
   - "beetle_images_resized/*.jpg"
+- config_name: individual_specimens
+  data_files:
+  - "individual_specimens.csv"
+  - "individual_specimens/part_000/*.png"
+  - "individual_specimens/part_001/*.png"
 - config_name: "separate segmented splits"
   data_files:
   - "Separate_segmented_train_test_splits_80_20/*/*/*.jpg"
@@ -183,6 +188,16 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - See notebooks in the [Beetle Processing Repository](https://github.com/Imageomics/2018-NEON-beetles-processing) for more information and analyses of these values, addition and renaming of the above columns from the [original measurement CSV](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/blob/bbefad05d50ed55da82e99bd330afe12a5fd1d97/BeetleMeasurements.csv), and the creation of the individual metadata CSV.
   - `beetle_images_resized/metadata.csv` has `pictureID`, `scientificName`, `genus`, `species`, `NEON_sampleID`, `siteID`, and `file_name` columns to display the resized images in the dataset viewer with some group image-level information. It will match up to information from `BeetleMeasurments.csv` on `pictureID`, though this is _not_ a unique alignment since it's not a unique ID for `BeetleMeasurements.csv`, but is for the resize.
 
+
+**individual_specimen.csv**: This CSV was created for individually cropped images.
+  - `individualImageFilePath`: Relative path to individual image from the root of the directory (`individual_specimens/part_<part_number>/<pictureID>_specimen_<number>.png`). The `number` corresponds to the position of the beetle specimen within the group image, numbered from left to right and top to bottom.
+  - `groupImageFilePath`: Relative path to group image from the root of the directory (`group_images/<pictureID>.jpg`)
+  - `NEON_sampleID`: NEON identifier for the sample (576 unique IDs), prefixed by the `plotID`. (Matches `NEON_sampleID` in `BeetleMeasurements.csv`.)
+  - `scientificName`: Binomial scientific name of the specimen.
+  - `siteID`: String. Identifier for the site from which the specimens were collected. There 30 different site IDs. For more information on the sites, visit: https://www.neonscience.org/field-sites/explore-field-sites.
+  - `site_name`: Name of field site from which the specimens were collected. There are 43 different field site names. -- These lack consistency (sometimes "NEON" or "Site" was used in the name causing duplicates), and will be updated using the site codes.
+  - `plotID`: Identifier for the plot from which the specimens were collected (`<siteID>_<plot number>`). Each site has multiple plots; there are 144 total plots from which specimens were collected.
+
 **Separate_segmented_train_test_splits_80_20/metadata.csv**: metadata file for the segmented individuals in the `Separate_segmented_train_test_splits_80_20` folder.
   - `filename`: name of image file (`beetle_<number code>.png`).
   - `md5`: MD5 hash of the image (unique identifier).