Datasets:

imageomics
/

2018-NEON-beetles

@@ -53,3 +53,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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	@@ -0,0 +1,3 @@

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+A00000034539.jpg,beetle_images_resized/A00000034539.jpg
+A00000050040.jpg,beetle_images_resized/A00000050040.jpg
+A00000003356.jpg,beetle_images_resized/A00000003356.jpg
+A00000046178.jpg,beetle_images_resized/A00000046178.jpg

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+---
+license: cc-by-sa-4.0
+language:
+- en
+pretty_name: 2018 NEON Ethanol-preserved Ground Beetles
+task_categories:
+- image-classification
+- image-segmentation
+tags:
+- biology
+- image
+- animals
+- CV
+- beetles
+- elytra
+- elytra width
+- elytra length
+- size
+size_categories:
+- n<1K
+- 10K<n<100K
+configs:
+- config_name: group_images
+  data_files:
+  - "BeetleMeasurements.csv"
+  - "group_images/*.jpg"
+- config_name: resized_images
+  data_files:
+  - "BeetleMeasurements_resized.csv"
+  - "beetle_images_resized/*.jpg"
+---
+<!-- - 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 collected from various NEON sites in 2018 and photographed in batches in 2022.
+## Dataset Details
+### Dataset Description
+- **Curated by:** I.E. Fluck, B. Baiser, R. Cholesky, 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)
+<!-- - **Paper:** -->
+<!-- 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 [Zooniverse]().
+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.-->
+<!--
+### Supported Tasks and Leaderboards
+[More Information Needed]
+<!-- Provide benchmarking results -->
+## Dataset Structure
+<!-- 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. -->
+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.
+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`.
+```
+/dataset/
+    group_images/
+        <pictureID 1>.jpg
+        <pictureID 2>.jpg
+        ...
+        <pictureID 577>.jpg
+    beetle_images_resized/
+        <pictureID 1>.jpg
+        <pictureID 2>.jpg
+        ...
+        <pictureID 577>.jpg
+    individual_images/
+        <individualID 1>.jpg
+        <individualID 2>.jpg
+        ...
+        <individualID 11459>.jpg
+    BeetleMeasurements.csv
+    BeetleMeasurements_resized.csv
+    individual_metadata.csv
+```
+### Data Instances
+[More Information Needed]
+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](). -->
+Segmentation was completed by adapting the elytra length and width annotations to generate expected bounding boxes. [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).
+|![picture of beetles in A00000046094](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/group_images/A00000046094.jpg)|
+|:--|
+|Image of _Carabus goryi_ beetles from sample A00000046094.|
+### Data Fields
+**BeetleMeasurements.csv**:
+  - `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, 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_straight`: 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 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`.
+  - `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.
+  - `user_name`: Zooniverse username of person annotating the elytra length and width information (there were 3 annotators).
+  - `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 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.
+**NOTE:**
+  - 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.
+  - 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.
+  - `BeetleMeasurements_resized.csv` has just `pictureID` and `file_name` columns to display the resized images in the dataset viewer. 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.
+**TODO:* Make individual metadata CSV file:
+**individual_metadata.csv**:
+  - `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`.)
+  - `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 1](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/beetles.png)|
+|:--|
+|**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
+This dataset does not have train-test splits.
+## 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.
+### Source Data
+<!-- This section describes the source data (e.g., news text and headlines, social media posts, translated sentences, ...). As well as an original source it was created from (e.g., sampling from Zenodo records, compiling images from different aggregators, etc.) -->
+The specimens come from [NEON sites](https://www.neonscience.org/field-sites/explore-field-sites), as indicated in the `BeetleMeasurements` CSV. They were identified by domain scientists (beetle experts) based on physical examination. Each sample consists of a single species. For more information about general NEON data, please see their [Ground beetles sampled from pitfall traps page](https://data.neonscience.org/data-products/DP1.10022.001).
+The samples were sent from NEON, preserved in ethanol, then arranged on a lattice to be photographed. Isadora Fluck photographed the beetles in each sample in 2022, using a Nikon D500 with lens: AF-S Micro NIKKOR 60mm 1:2.8G ED (Nikon).
+#### 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.
+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.
+ -->
+The beetles were preserved in ethanol following collection from NEON sites in 2018. They were were sent by [NEON](https://www.neonscience.org/) to 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
+<!--
+If the dataset contains annotations which are not part of the initial data collection, use this section to describe them.
+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 Zooniverse by Isadora Fluck and two 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
+[More Information Needed: URL for Zooniverse?]
+<!-- 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 Zooniverse. 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. -->
+- Isadora E. Fluck: Ph.D. Candidate at Baiser Lab of Community Ecology University of Florida annotated all samples, and led annotation effort of two summer REU students:
+  - Riley Wolcheski
+  - Isha Chinniah
+### Personal and Sensitive Information
+<!--
+For instance, if your data includes people or endangered species. -->
+N/A
+## Considerations for Using the Data
+<!--
+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".
+-->
+  - 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 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.
+### Bias, Risks, and Limitations
+[More Information Needed]
+<!-- This section is meant to convey both technical and sociotechnical limitations. Could also address misuse, malicious use, and uses that the dataset will not work well for.-->
+This dataset does not have a balanced representation of genera.
+<!-- For instance, if your data exhibits a long-tailed distribution (and why). -->
+### Recommendations
+Be aware of the distribution when determining use cases and metrics for evaluation.
+<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
+## Licensing Information
+This dataset is licensed under [CC BY-SA](https://creativecommons.org/licenses/by-sa/4.0/).
+## Citation
+**BibTeX:**
+**Data**
+```
+@misc{Fluck2018_NEON_Beetle,
+  author = {I.E. Fluck and B. Baiser and R. Cholesky and I. Chinniah and S. Record},
+  title = {2018 NEON Ethanol-preserved Ground Beetles},
+  year = {2024},
+  url = {https://huggingface.co/datasets/imageomics/2018-NEON-beetles},
+  doi = {<doi once generated>},
+  publisher = {Hugging Face}
+}
+```
+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.
+<!--
+## Glossary
+<!-- [optional] If relevant, include terms and calculations in this section that can help readers understand the dataset or dataset card. -->
+<!--
+## More Information
+<!-- [optional] Any other relevant information that doesn't fit elsewhere. -->
+## Dataset Card Authors
+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. -->