Adding Manually cropped individual samples

README.md

@@ -12,48 +12,48 @@ tags:
 - animals
 - CV
 - beetles
-- Carabidae
-- ground beetles
 - elytra
 - elytra width
 - elytra length
 - size
 size_categories: 
 - n<1K
-- 1K<n<10K
 - 10K<n<100K
 configs:
 - config_name: group_images
   data_files:
   - "group_images/metadata.csv"
   - "group_images/*.jpg"
-- config_name: group_images_resized
+- config_name: group_images_masks
   data_files:
-  - "group_images_resized/metadata.csv"
-  - "group_images_resized/*.jpg"
-- config_name: individual_specimens
+  - "group_images_masks/metadata.csv"
+  - "group_images_masks/*.png"
+- config_name: resized_images
   data_files:
-  - "individual_specimens/metadata.csv"
-  - "individual_specimens/part_000/*.png"
-  - "individual_specimens/part_001/*.png"
-  default: true
+  - "beetle_images_resized/metadata.csv"
+  - "beetle_images_resized/*.jpg"
 - config_name: "separate segmented splits"
   data_files:
   - "Separate_segmented_train_test_splits_80_20/*/*/*.jpg"
   - "Separate_segmented_train_test_splits_80_20/metadata.csv"
-description: "Collection of ethanol-preserved ground beetles (family Carabidae) collected from various NEON sites in 2018 and photographed in batches in 2022. This dataset contains both group and individual specimen images (individuals segmented from the group images). Elytra measurements of the beetle specimens (taken on the images) are also provided."
 ---
+<!-- - config_name: individual_images
+  data_files:
+  - "individual_metadata.csv"
+  - "individual_images/*.jpg"
+--- -->
+
 
 # Dataset Card for 2018 NEON Ethanol-preserved Ground Beetles
 
 <!-- Provide a quick summary of what the dataset is or can be used for. --> 
-Collection of ethanol-preserved ground beetles (family Carabidae) collected from various NEON sites in 2018 and photographed in batches in 2022. This dataset contains both group and individual specimen images (individuals segmented from the group images). Elytra measurements of the beetle specimens (taken on the images) are also provided.
+Collection of ethanol-preserved ground beetles (family Carabidae) collected from various NEON sites in 2018 and photographed in batches in 2022.
 
 ## Dataset Details
 
 ### Dataset Description
 
-- **Curated by:** I.E. Fluck, I. Chinniah, R. Wolcheski, M. Khurana, SM Rayeed, B. Baiser, E.G. Campolongo, A. Karpatne, C.V. Stewart, and S. Record
+- **Curated by:** I.E. Fluck, B. Baiser, R. Wolcheski, I. Chinniah, and S. Record
 <!-- 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:** [Imageomics/2018-NEON-beetles-processing](https://github.com/Imageomics/2018-NEON-beetles-processing)
@@ -61,9 +61,9 @@ Collection of ethanol-preserved ground beetles (family Carabidae) collected from
 
 
 <!-- Provide a longer summary of what this dataset is. -->
-This dataset is composed of a collection of 577 images of ethanol-preserved beetles collected at [NEON](https://www.neonscience.org/) sites in 2018. Each image contains a collection of beetles of the same species from a single plot at the labeled site. In 2022, they were arranged on a lattice and photographed; the elytra length and width were then annotated for each individual in each image using [Notes from Nature](https://www.zooniverse.org/organizations/md68135/notes-from-nature), a project on the [Zooniverse platform](https://www.zooniverse.org/). 
+This dataset is composed of a collection of 577 images of ethanol-preserved beetles collected at [NEON](https://www.neonscience.org/) sites in 2018. Each image contains a collection of beetles of the same species from a single plot at the labeled site. In 2022, they were arranged on a lattice and photographed; the elytra length and width were then annotated for each individual in each image using [Zooniverse](). 
 
-The individual images were segmented out based on scaling the elytra measurement pixel coordinates to the full-size images (more information on this process is available on the [Imageomics/2018-NEON-beetles-processing](https://github.com/Imageomics/2018-NEON-beetles-processing) repository).
+The individual images were segemented out based on scaling the elytra measurement pixel coordinates to the full-size images (more information on this process is available on the [Imageomics/2018-NEON-beetles-processing](https://github.com/Imageomics/2018-NEON-beetles-processing) repository).
 
 <!--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.-->
 
@@ -78,13 +78,19 @@ The individual images were segmented out based on scaling the elytra measurement
 
 <!-- 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. -->
 
-This dataset has 4 subsets, which are described in greater detail below in [Data Instances](#data-instances):
+In `group_images` we have 577 images of multiple beetles in a reasonably regular pattern (see sample image below). Each of these images contains a centimeter-based scalebar and a barcode representing the sample (collection of beetles in the image). Each row in `BeetleMeasurements.csv` corresponds to a measurement of the elytra (length or width) of an individual beetle.
+
+`Separate_segmented_train_test_splits_80_20` contains individual images of 11 different species of beetles. There are 12 folders, but melanarius melanarius is a subspecies designation for melanarius, so it should not be considered a species distinction. These images are divided into an 80-20 train-test split, and further separated into subfolders based on their species (as shown below).
 
-1. `group_images`: all 577 orignal full size images.
-2. `group_images_resized`: all 577 resized (approximately 1MB) group images used for annotation in Notes from Nature (1MB was the size limitation imposed by the software); aspect ratio was maintained in the resize.
-3. `individual_specimens`: all 11,654 individuals from the `group_images`, segmented _manually_ to have one image per individual.
-4. `separate segmented splits`: 7,070 individual beetle images segmented from the `group_images` as part of [BeetlePalooza 2024](https://doi.org/10.5281/zenodo.15540300). These images were organized into an 80-20 train-test split and are in the `Separate_segmented_train_test_splits_80_20/` directory.
+<!-- Still to be added:
+The `individual_images` directory contains images of each individual segmented from the group images. These connect back to their group image based on the `individualID`.
 
+    individual_images/
+        <individualID 1>.jpg
+        <individualID 2>.jpg
+        ...
+        <individualID 11459>.jpg
+-->
 ```
 /dataset/
     group_images/
@@ -93,7 +99,13 @@ This dataset has 4 subsets, which are described in greater detail below in [Data
         ...
         <pictureID 577>.jpg
         metadata.csv
-    group_images_resized/
+    group_images_masks/
+        <pictureID 1>_masks.jpg
+        <pictureID 2>_masks.jpg
+        ...
+        <pictureID 577>_masks.jpg
+        metadata.csv
+    beetle_images_resized/
         <pictureID 1>.jpg
         <pictureID 2>.jpg
         ...
@@ -111,36 +123,30 @@ This dataset has 4 subsets, which are described in greater detail below in [Data
             ...
             <species 12>/
         metadata.csv
-        README.md    # information about this subset of the dataset
-    individual_specimens/
-        part_000/
-            <pictureID>_specimen_<number>.png
-            ...
-        part_001/
-            <pictureID>_specimen_<number>.png
-            ...
-        metadata.csv
+    separate_segmented_beetle_images/
+        <pictureID 1>.jpg
+        <pictureID 2>.jpg
+        ...
     BeetleMeasurements.csv
+    individual_metadata.csv
 ```
 
 
+
 ### Data Instances
+[More Information Needed]
 
-This dataset has 4 subsets:
+The `group_images` folder has all 577 orignal full size images. The `beetle_images_resized` folder has the resized (approximately 1MB) images used for annotation in Zooniverse (1MB was the size limitation imposed by the software); aspect ratio was maintained in the resize. <!-- >, and the code used can be found [here](). -->
 
-1. `group_images`: 577 images of multiple beetles in a reasonably regular pattern (see sample image below). Each of these images contains a centimeter-based scalebar and a barcode representing the sample (collection of beetles in the image). Each row in `BeetleMeasurements.csv` corresponds to a measurement of the elytra (length or width) of an individual beetle.
-2. `group_images_resized`: All 577 `group_images` resized to the dimensions required for Notes from Nature annotation. These resized images align with the individual measurements provided in `BeetleMeasurements.csv`, unlike the images in the `group_images` subset, which require conversion that the pixel locations are converted to match the full size images.
-3. `individual_specimens`: 11,654 manually segmented images of all individual specimens photographed in the `group_images` subset. These images are split between two folders (`part_000/` and `part_001/`), and are labeled based on the group image to which they belong (`pictureID`), then the associated specimen when labeling within the tray from left to right, top to bottom (as if reading a book). Metadata for these images can be aligned using the `individual_specimens/metadata.csv`.
-4. `separate segmented splits`: 7,070 individual beetle images segmented from the `group_images`. This subset encompasses 11 different species of beetles. There are 12 folders, but _melanarius melanarius_ is a subspecies designation for _melanarius_, so it should not be considered a species distinction. These images are divided into an 80-20 train-test split, and further separated into subfolders based on their species (as shown below). These images are all contained in the `Separate_segmented_train_test_splits_80_20/` directory, and were generated as part of [BeetlePalooza 2024](https://doi.org/10.5281/zenodo.15540300). See [`Separate_segmented_train_test_splits_80_20/README`](Separate_segmented_train_test_splits_80_20/README.md) for more details. 
-    - The code used to produce the images and splits in `Separate_segmented_train_test_splits_80_20/` is provided [here](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Beetle_Palooza_image_separation.ipynb).
+The code used to produce the images and splits in `Separate_segmented_train_test_splits_80_20/` is provided [here](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Beetle_Palooza_image_separation.ipynb).
 
 <!-- images not provided here
 Segmentation was completed by adapting the elytra length and width annotations to generate the xy point input for the [Segment Anything (SAM)]() model. [Segment Anything (SAM)]() was then used to segment the individual beetles. More information and the code for this process is provided in the [Imageomics/2018-NEON-beetles-processing repo](https://github.com/Imageomics/2018-NEON-beetles-processing).
 -->
 
-|![Figure 1, picture of beetles in A00000046094, an image in the group images subset](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/group_images/A00000046094.jpg)| 
+|![picture of beetles in A00000046094](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/group_images/A00000046094.jpg)| 
 |:--|
-|**Figure 1.** Image of _Carabus goryi_ beetles from sample A00000046094. This image is part of the `group_images` subset.|
+|Image of _Carabus goryi_ beetles from sample A00000046094.|
 
 
 ### Data Fields
@@ -149,11 +155,11 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - `pictureID`: Name of the image (`<sample-barcode>.jpg`, though sometimes it's `<NEON_sampleID_>`.jpg); this matches the barcode on the sample bottle (included in the image). Unique identifier for the 577 _group_ images, not for dataset. There are 11,459 individual beetles. All individuals in a single image are from the same location and are the same species. However, there is one image (`MOAB_001.S.20180724.jpg`) with 17 individuals that does not have any taxonomic information. 10 individuals do not have species-level labels
   - `scalebar`: Pixel coordinates indicating the beginning and end of one side of a 1cm square on the ruler/scalebar in the image. This is indicated by two points `p1 = (x1, y1)` and `p2 = (x2, y2)`, such that the Euclidean distance between them is the number of pixels in one centimeter.
   - `cm_pix`: Integer. The number of pixels in a centimeter on the scalebar (measured by Euclidean distance between points given in `scalebar`).
-  - `individual`: Integer. The beetle in the image to whom the measurements refer. The beetles are measured "in line" (numbering is from left to right, top to bottom, as one would read a book). However, Notes from Nature does not register individual IDs beyond 99 (once 99 individuals are marked, it restarts the count at 1). Be careful with it.
+  - `individual`: Integer. The beetle in the image to whom the measurements refer. The beetles are measured "in line" (numbering is from left to right, top to bottom, as one would read a book). However, Zooniverse does not register individual IDs beyond 99 (once 99 individuals are marked, it restarts the count at 1). Be careful with it.
   - `structure`: Whether the measurement applies to the length or width of the elytra (`ElytraLength` or `ElytraWidth`, respectively). 
   - `lying_flat`: Whether or not the beetle is lying _flat_ in the image (`Yes` or `No`). This does _NOT_ correlate to vertical or horizontal alignment; it is whether the individual is twisted to one side or not--a side effect of how they died. Generally, the measured width will be shorter than the true width if this is `No`.
   - `coords_pix`: Pixel coordinates of the line marking the length or width of the elytra (green or purple line in the sample image). Note that these annotations were done on the resized copy of the image (1MB), but the aspect ratio was maintained in the resizing.
-  - `dist_pix`: Float. The length or width of the elytra (indicated by `structure`) as measured in pixels (calculated as Euclidean distance between `coords_pix` points).
+  - `dist_pix`: Float. The length or width of the elytra (indicated by `structure`) as measured in pixels (calculated as Euclidean distance beetween `coords_pix` points).
   - `dist_cm`: Float. The length or width of the elytra (indicated by `structure`) as measured in centimeters using the scalebar compared to the measured pixel distance (`dist_pix/cm_pix`).
   - `scientificName`: Scientific name of the specimen (`<Genus> <species>`). There are 78 different species among 36 genera, though another 10 individuals are only labeled to the genus (or subgenus) level. The 17 individuals in `PictureID` `MOAB_001.S.20180724.jpg` are missing the scientific name label (they are all the same species). These labels were provided by NEON.
   - `NEON_sampleID`: NEON identifier for the sample (576 unique IDs), prefixed by the `plotID`. 
@@ -161,10 +167,10 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - `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.
   - `user_name`: Zooniverse username of person annotating the elytra length and width information (there were 3 annotators).
-  - `workflowID`: Integer identifier for the Notes from Nature workflow used. There are 5.
+  - `workflowID`: Integer identifier for the Zooniverse workflow used. There are 5.
   - `genus`: Genus of the individual (generated by taking the first word in the `scientificName`). There are 36 unique genera labeled.
   - `species`: Species of the individual (generated from the word(s) following the `genus` in the `scientificName`). There are 78 unique species labeled.
-  - `combinedID`: Generated from `PictureID` (minus the `.jpg`) plus `_<individual>`. This gives only 11,104 IDs, as it suffers from the issue of `individual` based on Notes from Nature's export. Individuals should be measured by half the number of rows with `user_name == "IsaFluck"`.
+  - `combinedID`: Generated from `PictureID` (minus the `.jpg`) plus `_<individual>`. This gives only 11,104 IDs, as it suffers from the issue of `individual` based on Zooniverse's export. Individuals should be measured by half the number of rows with `user_name == "IsaFluck"`.
   - `measureID`: Unique identifier for the beetle measurements (and this CSV), generated using the `uuid` package. There are 39,064 unique measurements (2 per beetle, with overlap on 234 images annotated by all three annotators and 1 annotated by just two).
   - `file_name`: Relative path to image from the root of the directory (`<group_images>/<pictureID>.jpg`); allows for image to be displayed in the dataset viewer alongside its associated metadata.
   - `image_dim`: Dimensions of full-sized image `(<height>, <width>, <number of channels>)`.
@@ -177,29 +183,31 @@ 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/metadata.csv**: This CSV was created for individually cropped images.
-  - `file_name`: Relative path _from metadata file location_ to images for dataset viewer functionality (`part_<part_number>/<pictureID>_specimen_<number>.png`); displays the image in the viewer.
-  - `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.
-  - `individualImageFilePath`: Relative path to individual image from the _root of the repository_ (`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 repository_ (`group_images/<pictureID>.jpg`)
-
 **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).
-  - `species`: species epithet of the beetle in the image. **Note:** _melanarius melanarius_ is a subspecies designation of _melanarius_. Genera are as described [here](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/discussions/18#67bcabad85e7281434139a8a), full alignment should be possible with the [generation code](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Beetle_Palooza_image_separation.ipynb).
+  - `species`: species epithet of the beetle in the image. _Note:_ melanarius melanarius is a subspecies designation of melanarius. Genera are as described [here](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/discussions/18#67bcabad85e7281434139a8a), re-alignment is pending.
   - `split`: `train` or `test`, 80\% of the images  are in the training set.
   - `file_name`: path to the image from the `Separate_segmented_train_test_splits_80_20` folder to display in the dataset viewer.
   - `subset`: label given to this subset of the full image dataset (as selected in the viewer): `separate segmented splits`.
 
+**individual_metadata.csv**: This CSV was created for individual images that have not yet been added to this repository.
+  - `individualID`: ID of beetle in the individual image (`<measureID_length>_<measureID_width>`). This is a unique identifier for this CSV.
+  - `combinedID`: Generated from `PictureID` (minus the `.jpg`) plus `_<individual>`. (Matches `combinedID` in `BeetleMeasurements.csv`.)
+  - `lying_flat`: Whether or not the beetle is lying _flat_ in the image (`Yes` or `No`). This does _NOT_ correlate to vertical or horizontal alignment; it is whether the individual is twisted to one side or not--a side effect of how they died. Generally, the measured width will be shorter than the true width if this is `No`.
+  - `elytraLength`: Length of the elytra in centimeters. Indicated by the green line in the image below.
+  - `elytraWidth`: Width of the elytra in centimeters. Indicated by the purple line in the image below.
+  - `measureID_length`: `measureID` from `BeetleMeasurements.csv` for the `elytraLength` of this individual. Can be used to fetch measure-specific information from `BeetleMeasurements.csv`.
+  - `measureID_width`: `measureID` from `BeetleMeasurements.csv` for the `elytraWidth` of this individual. Can be used to fetch measure-specific information from `BeetleMeasurements.csv`.
+  - `genus`: Genus of the individual (generated by taking the first word in the `scientificName` from `BeetleMeasurements.csv`). There are 36 unique genera labeled.
+  - `species`: Species of the individual (generated from the word(s) following the `genus` in the `scientificName` from `BeetleMeasurements.csv`). There are 78 unique species labeled.
+  - `NEON_sampleID`: NEON identifier for the sample (576 unique IDs), prefixed by the `plotID`. (Matches `NEON_sampleID` in `BeetleMeasurements.csv`.)
+  - `file_name`: Relative path to image from the root of the directory (`individual_images/<individualID>.jpg`); allows for image to be displayed in the dataset viewer alongside its associated metadata.
+
 
-|![Figure 2 example image of the annotations overlayed on the images](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/beetles.png)|
+|![Figure 1](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/beetles.png)|
 |:--|
-|**Figure 2.** Sample image of beetles with green and purple lines to indicate the measurement used for the elytra length and width, respectively. The red line marks the pixels for 1cm.|
+|**Figure 1.** Sample image of beetles with green and purple lines to indicate the measurement used for the elytra length and width, respectively. The red line marks the pixels for 1cm.|
 
 
 ### Data Splits
@@ -208,12 +216,11 @@ This dataset has a subset of the group images segmented to individuals and divid
 ## Dataset Creation
 
 ### Curation Rationale
+[More Information Needed]
 <!-- Motivation for the creation of this dataset. For instance, what you intended to study and why that required curation of a new dataset (or if it's newly collected data and why the data was collected (intended use)), etc. -->
 
 This dataset was curated for use at [BeetlePalooza 2024](https://github.com/Imageomics/BeetlePalooza-2024/wiki) to help drive scientific discovery through machine learning and computer vision.
 
-Further segmentation was completed to facilitate trait-based analysis at the individual level.
-
 
 ### Source Data
 
@@ -242,7 +249,7 @@ NEON (National Ecological Observatory Network). Ground beetles sampled from pitf
 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.
  -->
 
-This dataset is a collection of images taken from beetles collected by [NEON](https://www.neonscience.org/) field technicians that were preserved in ethanol following collection from NEON sites in 2018. A subset of difficult to ID taxa were pinned and sent to experts for identification. The images provided here were of more common species that did not require expert ID that could be identified by NEON field technicians. After being preserved in ethanol, the beetles were archived at the [NEON Biorepository](https://biorepo.neonscience.org/portal/). They were sent by Nico Franz, Kelsey Yule, and Andrew Johnston from the NEON Biorepository to Ben Baiser, Sydne Record, and Isadora Fluck for imaging in 2022. Information regarding the sites from which they were collected and the taxonomic labels were provided by NEON. Site information (names and ecoclimatic domains) can be matched to `siteID` from the `NEON_Field_Site_Metadata_20240802.csv`, which is available on [NEON's field sites information page](https://www.neonscience.org/field-sites/explore-field-sites) (click `Download Field Site Table (CSV)`).
+This dataset is a collection of images taken from beetles collected by [NEON](https://www.neonscience.org/) field technicians that were preserved in ethanol following collection from NEON sites in 2018. A subset of difficult to ID taxa were pinned and sent to experts for identification. The images provided here were of more common species that did not require expert ID that could be identified by NEON field technicians. After being preserved in ethanol, the beetles were archived at the [NEON Biorepository] (https://biorepo.neonscience.org/portal/). They were were sent by Nico Franz, Kelsey Yule, and Andrew Johnston from the NEON Biorepository to Ben Baiser, Sydne Record, and Isadora Fluck for imaging in 2022. Information regarding the sites from which they were collected and the taxonomic labels were provided by NEON. Site information (names and ecoclimatic domains) can be matched to `siteID` from the `NEON_Field_Site_Metadata_20240802.csv`, which is available on [NEON's field sites information page](https://www.neonscience.org/field-sites/explore-field-sites) (click `Download Field Site Table (CSV)`).
 
 
 ### Annotations
@@ -251,12 +258,12 @@ If the dataset contains annotations which are not part of the initial data colle
 
 Ex: We standardized the taxonomic labels provided by the various data sources to conform to a uniform 7-rank Linnean structure. (Then, under annotation process, describe how this was done: Our sources used different names for the same kingdom (both _Animalia_ and _Metazoa_), so we chose one for all (_Animalia_). -->
 
-Annotations (elytra length and width) were completed in Notes from Nature by Isadora Fluck and two Harvard Forest summer REU students (Riley Wolcheski and Isha Chinniah); annotator is indicated by their NEON system usernames in the `BeetleMeasurements` CSV. The annotations (2 per beetle) were repeated for a subset of the images to measure observation error introduced in the annotation process. The taxonomic labels were provided by NEON with the samples.
+Annotations (elytra length and width) were completed in Zooniverse by Isadora Fluck and two Harvard Forest summer REU students (Riley Wolcheski and Isha Chinniah); annotator is indicated by their NEON system usernames in the `BeetleMeasurements` CSV. The annotations (2 per beetle) were repeated for a subset of the images to measure observation error introduced in the annotation process. The taxonomic labels were provided by NEON with the samples.
 
 #### Annotation process
 <!-- This section describes the annotation process such as annotation tools used, the amount of data annotated, annotation guidelines provided to the annotators, interannotator statistics, annotation validation, etc. -->
 
-The images were downsized to 1MB (preserving aspect ratio) for annotation in [Notes from Nature](https://www.zooniverse.org/organizations/md68135/notes-from-nature). Overall, 234 images were annotated by all three annotators and 1 was annotated by just two. Beetles were indicated as not lying flat if they tended to one or the other side, as this can result in a smaller width measurement than expected. See the [sample image](https://huggingface.co/datasets/imageomics/BeetlePalooza/blob/main/beetles.png) (also in Figure 2) for indicators of length and width, as well as the centimeter mark in pixels on the scalebar.
+The images were downsized to 1MB (preserving aspect ratio) for annotation in [Zooniverse](https://www.zooniverse.org/). Overall, 234 images were annotated by all three annotators and 1 was annotated by just two. Beetles were indicated as not lying flat if they tended to one or the other side, as this can result in a smaller width measurement than expected. See the [sample image](https://huggingface.co/datasets/imageomics/BeetlePalooza/blob/main/beetles.png) (also in Figure 1) for indicators of length and width, as well as the centimeter mark in pixels on the scalebar.
 
 #### Who are the annotators?
 <!-- This section describes the people or systems who created the annotations. -->
@@ -277,7 +284,7 @@ Things to consider while working with the dataset. For instance, maybe there are
 -->
   - The `NEON_sampleID` RMNP_014.20180709.CALADV.01 is repeated because there were too many individuals in the sample to organize them all in one picture. Thus, the individuals from this sample are split between two pictures: `A00000051555_1` and `A00000051555_2`.
   - The `NEON_sampleID` MOAB_001.S.20180724 was provided without scientific name identification.
-  - The `individual` indicator is not unique to `pictureID` since Notes from Nature restarted IDs after individual number 99, so individuals are indicated by measurements annotated by `user_name == "IsaFluck"` since she annotated each image once, with the other annotators just labeling a subset for comparison.
+  - The `individual` indicator is not unique to `pictureID` since Zooniverse restarted IDs after individual number 99, so individuals are indicated by measurements annotated by `user_name == "IsaFluck"` since she annotated each image once, with the other annotators just labeling a subset for comparison.
   - These images do not include all beetles sampled at all sites in 2018 because they do not include the pinned specimens.
   - Dorsal images may not provide all the information needed to ID a beetle.
 
@@ -298,72 +305,26 @@ This dataset is licensed under [CC BY-SA](https://creativecommons.org/licenses/b
 
 ## Citation
 
-**Dataset**
+**BibTeX:**
 
-```bibtex
+**Data**
+```
 @misc{Fluck2018_NEON_Beetle,
-  author = {Isadora E. Fluck and Isha Chinniah and Riley Wolcheski and Mridul Khurana and S M Rayeed and Benjamin Baiser and
-            Elizabeth G. Campolongo and Anuj Karpatne and Charles V. Stewart and Sydne Record},
-  title = {2018 {NEON} Ethanol-preserved Ground Beetles (Revision a596e65)},
-  year = {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 = {2024},
   url = {https://huggingface.co/datasets/imageomics/2018-NEON-beetles},
-  doi = { 10.57967/hf/6890 },
+  doi = { 10.57967/hf/5252 },
   publisher = {Hugging Face}
 }
 ```
 
-If you use the `separate segmented splits` subset (images in `Separate_segmented_train_test_splits_80_20`), please follow the citation guidance in [`Separate_segmented_train_test_splits_80_20/README`](Separate_segmented_train_test_splits_80_20/README.md), which involves also citing the code repository ([Imageomics/2018-NEON-beetles-processing](https://github.com/Imageomics/2018-NEON-beetles-processing)) used to produce this subset of images.
-
-Please be sure to cite both the dataset and the source data (specimen collection), and include the NEON acknowledgements (provided below) in your work.
-
-**Source Data:**
-```bibtex
-@misc{Portal2022-ho,
-  title     = "{NEON} biorepository Carabid collection (trap sorting)",
-  author    = "{NEON Biorepository Portal}",
-  abstract  = "This collection contains subsamples of Carabid adults from pitfall sampling from a single trap (NEON sample class:
-               bet\_sorting\_in.subsampleID.bet). Ground beetles are sampled using pitfall traps (16 oz deli containers filled with 150 or
-               250 mL of propylene glycol). Four (pre-2018) or 3 (2018 and beyond) traps are deployed in each of 10 (pre-2023) or 6 (2023
-               and beyond) plots at each terrestrial NEON site, with traps arrayed approximately 20 meters from the center of the plot.
-               Sampling occurs biweekly throughout the growing season (when temperatures are above 4 degrees C). Following trap collection,
-               all beetles from the family Carabidae are sorted by NEON technicians and identified to species or morphospecies. A subset
-               of collected Carabidae are pointed or pinned, while other specimens (non-pinned/non-pointed carabids, invertebrate
-               bycatch, and vertebrate bycatch) are stored in 95\% ethanol for archiving. Regardless of storage method, all collections data
-               are reported at a per trap resolution. A subset of pinned ground beetles (up to 467 per site per year) are sent to an expert
-               taxonomist for secondary identification. Identifications performed on these individuals may be used to estimate
-               uncertainty in parataxonomist identification by NEON technicians.",
-  publisher = "National Ecological Observatory Network",
-  doi = {https://doi.org/10.15468/mjtykf},
-  note = {Accessed in 2022}
-}
-```
-
-```bibtex
-@misc{Portal2022-qu,
-  title     = "{NEON} Biorepository Carabid Collection (Archive Pooling)",
-  author    = "{NEON Biorepository Portal}",
-  abstract  = "This collection contains subsamples of Carabid adults from pitfall sampling and pooled across multiple traps within a plot
-               (NEON sample class: bet\_archivepooling\_in.subsampleID.bet). Ground beetles are sampled using pitfall traps (16 oz deli
-               containers filled with 150 or 250 mL of propylene glycol). Four (pre-2018) or 3 (2018 and beyond) traps are deployed in each of
-               10 (pre-2023) or 6 (2023 and beyond) plots at each terrestrial NEON site, with traps arrayed approximately 20 meters from the
-               center of the plot. Sampling occurs biweekly throughout the growing season (when temperatures are above 4 degrees C).
-               Following trap collection, all beetles from the family Carabidae are sorted by NEON technicians and identified to species or
-               morphospecies. A subset of collected Carabidae are pointed or pinned, while other specimens (non-pinned/non-pointed carabids,
-               invertebrate bycatch, and vertebrate bycatch) are stored in 95\% ethanol for archiving. A subset of pinned ground beetles (up to
-               467 per site per year) are sent to an expert taxonomist for secondary identification. Identifications performed on these
-               individuals may be used to estimate uncertainty in parataxonomist identification by NEON technicians.",
-  publisher = "National Ecological Observatory Network",
-  doi = {https://doi.org/10.15468/xicbza},
-  note = {Accessed in 2022}
-}
+If you use the individual segmented images, please also cite the code repository ([Imageomics/2018-NEON-beetles-processing](https://github.com/Imageomics/2018-NEON-beetles-processing)) used to produce them.
 
-```
 
 ## Acknowledgements
 
-The National Ecological Observatory Network is a program sponsored by the National Science Foundation and operated under cooperative agreement by Battelle. This material uses specimens and/or samples collected as part of the NEON Program. Additionally, this material is based upon work supported by the National Science Foundation under Award Numbers [2301322](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2301322&HistoricalAwards=false), [1950364](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1950364&HistoricalAwards=false), and [1926569](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1926569&HistoricalAwards=false), as well as the USDA National Institute of Food and Agriculture, Hatch Project [Number ME0-22425]() through the Maine Agricultural and Forest Experiment Station. Additional support was provided by the Imageomics Institute, which is supported by NSF [Award No. 2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) ([Imageomics](https://imageomics.org): 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 or the USDA National Institute of Food and Agriculture.
-
-We thank Michael Denslow and Robert P. Guralnick for their help in setting up and managing the annotation pipeline in Zooniverse.
+The National Ecological Observatory Network is a program sponsored by the National Science Foundation and operated under cooperative agreement by Battelle. This material uses specimens and/or samples collected as part of the NEON Program. Additionally, this material is based upon work supported by the National Science Foundation under Award Numbers [2301322](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2301322&HistoricalAwards=false), [1950364](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1950364&HistoricalAwards=false), and [1926569](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1926569&HistoricalAwards=false), as well as the USDA National Institute of Food and Agriculture, Hatch Project [Number ME0-22425]() through the Maine Agricultural and Forest Experiment Station. Additional support was provided by the Imageomics Institute, which is supported by NSF [Award No. 2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) ([Imageomics](https://imageomics.org): 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.
 
 <!-- 
 ## Glossary 
@@ -382,3 +343,4 @@ 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

@@ -1,52 +0,0 @@
-# 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.