Reorganize Repo

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).
@@ -343,4 +358,3 @@ Elizabeth G. Campolongo
 
 [More Information Needed--optional]
 <!-- Could include who to contact with questions, but this is also what the "Discussions" tab is for. -->
-

Separate_segmented_train_test_splits_80_20/README.md

@@ -0,0 +1,52 @@
+# Separate_segmented_train_test_splits_80_20
+
+This subset of the 2018 NEON Ethanol-preserved Ground Beetles dataset was generated as part of a project at [BeetlePalooza 2024](https://doi.org/10.5281/zenodo.15540300). The code to generate this collection of images is available in the [Beetle_Palooza_image_separation notebook](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Beetle_Palooza_image_separation.ipynb) provided in the [dataset processing repository](ttps://github.com/Imageomics/2018-NEON-beetles-processing). There were two directories of images generated during this processing [`group_images_masks/`](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/tree/7b3731daca1f91931f8086d6782ab9150ab8ce26/group_images_masks) and [`separate_segmented_beetle_images/`](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/tree/7b3731daca1f91931f8086d6782ab9150ab8ce26/separate_segmented_beetle_images), which have associated metadata files in the [metadata directory of the processing repo](https://github.com/Imageomics/2018-NEON-beetles-processing/tree/main/metadata); they are `group_images_masks_sb.csv` and `group_images_sb.csv`, respectively.
+
+## Citation
+
+If these or the final product (`Separate_segmented_train_test_splits_80_20`) are used, please cite both Revision 7b3731d of this dataset and the processing repository:
+
+Dataset [Revision 7b3731d](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/tree/7b3731daca1f91931f8086d6782ab9150ab8ce26):
+
+```
+@misc{isadora_e._fluck_2025,
+	author       = { Isadora E. Fluck and Benjamin Baiser and Riley Wolcheski and Isha Chinniah and Sydne Record },
+	title        = { 2018 {NEON} Ethanol-preserved Ground Beetles (Revision 7b3731d) },
+	year         = 2025,
+	url          = { https://huggingface.co/datasets/imageomics/2018-NEON-beetles },
+	doi          = { 10.57967/hf/5252 },
+	publisher    = { Hugging Face }
+}
+```
+
+Processing Repository:
+```
+@software{Ramirez_2018_NEON_Ethanol-preserved_2025,
+        author = {Ramirez, Michelle and Nepovinnykh, Ekaterina and Ali, Sarwan and Campolongo, Elizabeth G.},
+        doi = {10.5281/zenodo.16989738},
+        license = {MIT},
+        month = aug,
+        title = {{2018 NEON Ethanol-preserved Ground Beetles Processing}},
+        url = {https://github.com/Imageomics/2018-NEON-beetles-processing},
+        version = {2.0.0},
+        year = {2025}
+}
+```
+
+## About this Data Subset
+
+This folder contains cropped images of approximately 7,000 individual images for beetles from the following species (not really 12 species: repeated species epithet in _Pterostichus melanarius melanarius_ indicates this is the nominotypical subspecies of _Pterostichus melanarius_).
+1. _Calathus advena_
+2. _Cyclotrachelus torvus_
+3. _Chlaenius aestivus_
+4. _Euryderus grossus_
+5. _Harpalus pensylvanicus_ OR _Pterostichus pensylvanicus_ --- this species epithet seems to have two different genera associated to it and will thus require more effort for alignment. Hopefully, it's just a matter of merging on an ID from the original dataset but look at the filename generation to figure it out.
+6. _Pterostichus melanarius_
+7. _Pterostichus restrictus_
+8.  _Pterostichus melanarius melanarius_  —  nominotypical subspecies of _Pterostichus melanarius_
+9.  _Pterostichus lachrymosus_
+10.  _Carabus goryi_
+11.  _Cratacanthus dubius_
+12.  _Synuchus impunctatus_
+
+Please see the [processing notebook](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Beetle_Palooza_image_separation.ipynb) for more information on how these images were generated, and see the [metadata generation notebook](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Separate_segmented_splits_meta_gen.ipynb) for more information on the distribution of species.