Merge and edit AcuityView updates.

README.md

@@ -16,29 +16,28 @@ tags:
 - imbalanced
 - mimicry
 - cv
-pretty_name: Curated Gold Standard Cuthill Dataset
+pretty_name: Curated Gold Standard Hoyal Cuthill Dataset
 size_categories:
 - n<1K
 ---
-# Dataset Card for Curated Gold Standard Cuthill Dataset
+# Dataset Card for Curated Gold Standard Hoyal Cuthill Dataset
 
 ## Dataset Description
-Dorsal full body images of subspecies of Heliconius Erato and Heliconius Melpomene (18 subspecies total).
-960 images with 320 specimens
-Each image is a low-resolution ("images were then cropped and resized to a height of 64 pixels (maintaining the original image aspect ratio and padded to 140 pixels wide) Hoyal-Cuthill 2019 ) photographed in RGB 
-Low resolution images were then transformed using AccuityView (doi: https://cran.r-project.org/web/packages/AcuityView/index.html, 
-and estimates of accuity from: http://www.empiricalimaging.com/knowledge-base/acuityview/, https://www.annualreviews.org/doi/10.1146/annurev.ento.42.1.147
-Users should know that since Land 1997, more recent estimates of insect visual accuity have been created. 
-There are (3 images of each specimen Original/ Bird transformed/ Butterfly transformed).
-This data represents a subset subset of images processed from Cuthill, et. al. dataset available at [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978).
 
-Only Dorsal Images
+Dorsal full body images of subspecies of _Heliconius erato_ and _Heliconius melpomene_ (18 subspecies total).
+There are 960 images with 320 specimens (3 images of each specimen: Original/ Bird transformed/ Butterfly transformed)
+The original images are low-resolution RGB photographs (photographs were "cropped and resized to a height of 64 pixels (maintaining the original image aspect ratio and padded to 140 pixels wide)"(Hoyal Cuthill et al., 2019)).
+These low-resolution images were then transformed using [AcuityView](https://cran.r-project.org/web/packages/AcuityView/index.html) with estimates of acuity from [AcuityView 2.0](http://www.empiricalimaging.com/knowledge-base/acuityview/) and [Land, 1997](https://www.annualreviews.org/doi/10.1146/annurev.ento.42.1.147).
+Users should know that since Land (1997), more recent estimates of insect visual acuity have been created. 
 
-**Note:** `dorsal_images_cuthill` contains processed dorsal images from the original Cuthill dataset (all 1,234 specimens).
+This data represents a subset of images processed from Hoyal Cuthill et al. dataset available at [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978). Their original dataset also includes ventral images.
+
+
+**Note:** `dorsal_images_cuthill` contains processed dorsal images from the original Hoyal Cuthill dataset (all 1,234 specimens).
 
 - **Homepage:** 
 - **Repository:** [Butterfly-mimicry](https://github.com/Imageomics/Butterfly-mimicry) contains research done using this dataset.
-- **Paper:** 
+- **Paper:** [Imageomics Approach to Understanding Visual Biological Trait Similarities using Butterfly Mimicry as a Model System](http://rave.ohiolink.edu/etdc/view?acc_num=osu168198420667979)
 - **Leaderboard:** 
 - **Point of Contact:** 
 
@@ -52,7 +51,7 @@ This dataset card aims to be a base template for new datasets. It has been gener
 
 ### Supported Tasks and Leaderboards
 
-[More Information Needed]
+_Heliconius erato_ and _Heliconius melpomene_ subspecies identification (image classification), with variable settings for acuity of the observer (bird, butterfly, or human/other).
 
 ### Languages
 
@@ -127,7 +126,7 @@ English
 * Background: [210, 210, 210] (gray)
 * Fit in frame: Most padding is above and below the image, some on the left and right.
 * Ruler or Scale: None
-* Color (ColorChecker, white-balance, None): None
+* Color Reference (ColorChecker, white-balance, None): None
 
 
 ### Data Fields
@@ -141,16 +140,16 @@ English
 * `Subspecies`: subspecies of the specimen
 * `Sex`: sex of the specimen (male or female)
 * `addit_taxa_info`: additional taxonomic information (subspecies)
-* `type_stat`: [More Information Needed] 'ST', 'PT', or 'HT', but mostly null
+* `type_stat`: indicates "classical" or "example" specimen of species or subspecies ('ST', 'PT', or 'HT', indicating syntypes, paratypes, or holotypes, respectively). This field is mostly null.
 * `hybrid_stat`: hybrid status ('valid subspecies', 'subspecies synonym' or 'unknown' (only 1))
-* `in_reduced`: [More Information Needed] 0 or 1 to indicate yes or no
+* `in_reduced`: whether or not the specimen was used in the second analysis by Hoyal Cuthill et al. (1 or 0 to indicate yes or no, respectively). This was an effort to remove potential hybrids from their analysis; it does not always match our indication of hybrid status.
 * `locality`: where specimen was collected
 * `lat`: latitude where specimen was collected
 * `lon`: longitude where specimen was collected
 * `speciesdesig`: species designation, first initial of species '.' subspecies (eg., 'm. rosina')
 
 `Train_Test_Curated_GoldStandard_Hoyal_Cuthill.csv` has three additional columns:
-* `Image_filename_png`: filename of (png) image of specimen, `dorsal_images_cuthill/` + `<Image_filename_png>` is the filepath for the processed dorsal image
+* `Image_filename_png`: filename of (png) image of specimen, `dorsal_images_cuthill/  +   <Image_filename_png>` is the filepath for the processed dorsal image
 * `subset`: whether this is part of the training or test set (`train` or `test`)
 * `filepath`: the filepath for the train or test image
 
@@ -182,19 +181,18 @@ Processing steps included:
 ### Curation Rationale
 
 This dataset was curated for training a model to classify different species of Heliconius Butterflies and to take into account mimicry between species and acuity of the observer (bird, butterfly, or human/other).
-The original data (Cuthill et al 2019) had misclassified species/subspecies and some locality/ collection sites were outside the known range of the butterflies. 
+The original data (Hoyal Cuthill et al. 2019) had misclassified species/subspecies and some locality/ collection sites were outside the known range of the butterflies. 
 It also contained hybrid and aberrant samples, that had the potential to muddle classification results. 
 To prevent this, the data was further refined by several Heliconius experts to remove hybrid and aberrant samples. 
-Lastly, bird and butterfly acuities were added to provide another level of analysis using AccuityView and estimates of observer accuity.
+Lastly, bird and butterfly acuities were added to provide another level of analysis using [AcuityView](https://cran.r-project.org/web/packages/AcuityView/index.html) and estimates of observer acuity.
 
 
 ### Source Data
 
-Cuthill, et. al. [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978).
+Hoyal Cuthill et al. [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978).
 
 #### Initial Data Collection and Normalization
 
-[More Information Needed]
 Photographers: Robyn Crowther and Sophie Ledger, Natural History Museum, London.
 
 #### Who are the source language producers?
@@ -205,15 +203,15 @@ Photographers: Robyn Crowther and Sophie Ledger, Natural History Museum, London.
 
 #### Annotation process
 
-The original data has some misclassified species/subspecies, and had multiple hybrid samples. These samples were removed by hand by OM, CL, JM, KK. 
-Some localities were outside the known range of the butterflies, and were removed using QGIS and known sub species ranges. 
+The original data has some misclassified species/subspecies, and had multiple hybrid samples. These samples were removed by hand by Owen McMilan, Christopher Lawrence, Jim Mallet, Krzysztof Kozak. 
+Some localities were outside the known range of the butterflies, and were removed using QGIS and known subspecies ranges. 
 
 #### Who are the annotators?
 
-Christopher Lawrence 
-Jim Mallet
-Owen McMilan
-Krystof Kozak
+Christopher Lawrence, 
+Jim Mallet,
+Owen McMilan, and
+Krzysztof Kozak.
 
 ### Personal and Sensitive Information
 
@@ -227,7 +225,7 @@ N/A
 
 ### Discussion of Biases
 
-Biased towards species and subspecies within Heliconius. Focused on Heliconius erato and Heliconius melpomene 
+Biased towards species and subspecies within Heliconius. Focused on _Heliconius erato_ and _Heliconius melpomene_.
 
 ### Other Known Limitations
 
@@ -255,16 +253,46 @@ Biased towards species and subspecies within Heliconius. Focused on Heliconius e
 
 ### Licensing Information
 
-[More Information Needed]
+This work has been marked as dedicated to the public domain by applying the [CC0 Public Domain Waiver](https://creativecommons.org/publicdomain/zero/1.0/).
 
 ### Citation Information
 
-Krzysztof Kozak, Christopher Lawrence, James Mallet, Owen McMillan, David Carlyn, Mohannad Elhamod. (2023), "Curated_GoldStandard_Hoyal_Cuthill", https://huggingface.co/datasets/imageomics/Curated_GoldStandard_Hoyal_Cuthill.
+Krzysztof Kozak, Christopher Lawrence, James Mallet, Owen McMillan, David Carlyn, Mohannad Elhamod. (2023), "Curated GoldStandard Hoyal Cuthill", https://huggingface.co/datasets/imageomics/Curated_GoldStandard_Hoyal_Cuthill.
+
+Ramesh Babu, R. (2023). _Imageomics Approach to Understanding Visual Biological Trait Similarities using Butterfly Mimicry as a Model System_ [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu168198420667979
 
 Please also cite the original dataset from which this was adapted and its accompanying paper: 
 * Hoyal Cuthill, Jennifer F. et al. (2019), Data from: Deep learning on butterfly phenotypes tests evolution’s oldest mathematical model, Dryad, Dataset, https://doi.org/10.5061/dryad.2hp1978.
-* Hoyal Cuthill, Jennifer F. et al. (2019), Deep learning on butterfly phenotypes tests evolution’s oldest mathematical model, Science Advances, Article-journal, https://doi.org/10.1126/sciadv.aaw4967
+* Hoyal Cuthill, Jennifer F. et al. (2019), Deep learning on butterfly phenotypes tests evolution’s oldest mathematical model, Science Advances, Article-journal, https://doi.org/10.1126/sciadv.aaw4967.
+
+#### BibTeX
+
+Dataset:
+```
+@misc{CGSHC23,
+  author = {Krzysztof Kozak and Christopher Lawrence and James Mallet and Owen McMillan and David Carlyn and Mohannad Elhamod},
+  title = {Curated GoldStandard Hoyal Cuthill},
+  year = {2023},
+  url = {https://huggingface.co/datasets/imageomics/Curated_GoldStandard_Hoyal_Cuthill},
+  doi = {<doi once generated>},
+  publisher = {Hugging Face}
+}
+```
+
+Imageomics paper (Part of thesis work):
+```
+@masterthesis{ramesh_babu23,
+  title    = {Imageomics Approach to Understanding Visual Biological Trait Similarities using Butterfly Mimicry as a Model System},
+  author   = {Reshma Ramesh Babu},
+  year     =  2023,
+  month    = {May},
+  note     = {Available at \url{http://rave.ohiolink.edu/etdc/view?acc_num=osu168198420667979}},
+  school   = {The Ohio State University},
+  type     = {Master's thesis}
+}
+```
+
 
 ### Contributions
 
-The [Imageomics Institute](https://imageomics.org) is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) Institute program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning).
+The [Imageomics Institute](https://imageomics.org) is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) Institute program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning).