Update sample figure of annotations (#29)

- Update sample figure of annotations (7d2f949c0a38de36f4989275431358bd1326a256)
- Add source data (physical collection) citations (456b3a9f1de3e6f3a0ec4e794845365481ea7c2a)


Co-authored-by: Elizabeth Campolongo <[email protected]>

README.md

@@ -137,9 +137,9 @@ This dataset has 4 subsets:
 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).
 -->
 
-|![picture of beetles in A00000046094, an image in the group images subset](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/group_images/A00000046094.jpg)| 
+|![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)| 
 |:--|
-|Image of _Carabus goryi_ beetles from sample A00000046094. This image is part of the `group_images` subset.|
+|**Figure 1.** Image of _Carabus goryi_ beetles from sample A00000046094. This image is part of the `group_images` subset.|
 
 
 ### Data Fields
@@ -195,9 +195,9 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - `subset`: label given to this subset of the full image dataset (as selected in the viewer): `separate segmented splits`.
 
 
-|![Figure 1](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/beetles.png)|
+|![Figure 2 example image of the annotations overlayed on the images](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.|
+|**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.|
 
 
 ### Data Splits
@@ -254,7 +254,7 @@ Annotations (elytra length and width) were completed in Notes from Nature by Isa
 #### 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 1) 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 [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.
 
 #### Who are the annotators?
 <!-- This section describes the people or systems who created the annotations. -->
@@ -296,10 +296,9 @@ This dataset is licensed under [CC BY-SA](https://creativecommons.org/licenses/b
 
 ## Citation
 
-**BibTeX:**
+**Dataset**
 
-**Data**
-```
+```bibtex
 @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},
@@ -313,6 +312,50 @@ This dataset is licensed under [CC BY-SA](https://creativecommons.org/licenses/b
 
 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    = "Portal, Neon Biorepository",
+  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    = "Portal, Neon Biorepository",
+  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}
+}
+
+```
 
 ## Acknowledgements