egrace479 commited on
Commit
056a828
1 Parent(s): 643ca2c

Update README with full feature descriptions.

Browse files
Files changed (1) hide show
  1. README.md +19 -20
README.md CHANGED
@@ -23,9 +23,9 @@ size_categories:
23
  # Dataset Card for Curated Gold Standard Cuthill Dataset
24
 
25
  ## Dataset Description
26
- Dorsal full body images of subspecies of Heliconius Erato and Heliconius Melpomene (18 subspecies total).
27
  960 images with 320 specimens, each photographed in RGB with bird and butterfly acuity included (3 images of each specimen).
28
- Subset of images processed from Cuthill, et. al. dataset available at [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978).
29
 
30
  **Note:** `dorsal_images_cuthill` contains processed dorsal images from the original Cuthill dataset (all 1,234 specimens).
31
 
@@ -45,7 +45,7 @@ This dataset card aims to be a base template for new datasets. It has been gener
45
 
46
  ### Supported Tasks and Leaderboards
47
 
48
- [More Information Needed]
49
 
50
  ### Languages
51
 
@@ -120,7 +120,7 @@ English
120
  * Background: [210, 210, 210] (gray)
121
  * Fit in frame: Most padding is above and below the image, some on the left and right.
122
  * Ruler or Scale: None
123
- * Color (ColorChecker, white-balance, None): None
124
 
125
 
126
  ### Data Fields
@@ -134,16 +134,16 @@ English
134
  * `Subspecies`: subspecies of the specimen
135
  * `Sex`: sex of the specimen (male or female)
136
  * `addit_taxa_info`: additional taxonomic information (subspecies)
137
- * `type_stat`: [More Information Needed] 'ST', 'PT', or 'HT', but mostly null
138
  * `hybrid_stat`: hybrid status ('valid subspecies', 'subspecies synonym' or 'unknown' (only 1))
139
- * `in_reduced`: [More Information Needed] 0 or 1 to indicate yes or no
140
  * `locality`: where specimen was collected
141
  * `lat`: latitude where specimen was collected
142
  * `lon`: longitude where specimen was collected
143
  * `speciesdesig`: species designation, first initial of species '.' subspecies (eg., 'm. rosina')
144
 
145
  `Train_Test_Curated_GoldStandard_Hoyal_Cuthill.csv` has three additional columns:
146
- * `Image_filename_png`: filename of (png) image of specimen, `dorsal_images_cuthill/` + `<Image_filename_png>` is the filepath for the processed dorsal image
147
  * `subset`: whether this is part of the training or test set (`train` or `test`)
148
  * `filepath`: the filepath for the train or test image
149
 
@@ -175,7 +175,7 @@ Processing steps included:
175
  ### Curation Rationale
176
 
177
  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).
178
- The original data (Cuthill et al 2019) had misclassified species/subspecies and some locality/ collection sites were outside the known range of the butterflies.
179
  It also contained hybrid and aberrant samples, that had the potential to muddle classification results.
180
  To prevent this, the data was further refined by several Heliconius experts to remove hybrid and aberrant samples.
181
  Lastly, bird and butterfly acuities were added to provide another level of analysis.
@@ -183,11 +183,10 @@ Lastly, bird and butterfly acuities were added to provide another level of analy
183
 
184
  ### Source Data
185
 
186
- Cuthill, et. al. [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978).
187
 
188
  #### Initial Data Collection and Normalization
189
 
190
- [More Information Needed]
191
  Photographers: Robyn Crowther and Sophie Ledger, Natural History Museum, London.
192
 
193
  #### Who are the source language producers?
@@ -198,15 +197,15 @@ Photographers: Robyn Crowther and Sophie Ledger, Natural History Museum, London.
198
 
199
  #### Annotation process
200
 
201
- The original data has some misclassified species/subspecies, and had multiple hybrid samples. These samples were removed by hand by OM, CL, JM, KK.
202
- Some localities were outside the known range of the butterflies, and were removed using QGIS and known sub species ranges.
203
 
204
  #### Who are the annotators?
205
 
206
- Christopher Lawrence
207
- Jim Mallet
208
- Owen McMilan
209
- Krystof Kozak
210
 
211
  ### Personal and Sensitive Information
212
 
@@ -220,7 +219,7 @@ N/A
220
 
221
  ### Discussion of Biases
222
 
223
- Biased towards species and subspecies within Heliconius. Focused on Heliconius erato and Heliconius melpomene
224
 
225
  ### Other Known Limitations
226
 
@@ -248,7 +247,7 @@ Biased towards species and subspecies within Heliconius. Focused on Heliconius e
248
 
249
  ### Licensing Information
250
 
251
- [More Information Needed]
252
 
253
  ### Citation Information
254
 
@@ -256,8 +255,8 @@ Krzysztof Kozak, Christopher Lawrence, James Mallet, Owen McMillan, David Carlyn
256
 
257
  Please also cite the original dataset from which this was adapted and its accompanying paper:
258
  * 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.
259
- * 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
260
 
261
  ### Contributions
262
 
263
- 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).
 
23
  # Dataset Card for Curated Gold Standard Cuthill Dataset
24
 
25
  ## Dataset Description
26
+ Dorsal full body images of subspecies of _Heliconius erato_ and _Heliconius melpomene_ (18 subspecies total).
27
  960 images with 320 specimens, each photographed in RGB with bird and butterfly acuity included (3 images of each specimen).
28
+ Subset of images processed from Cuthill et al. dataset available at [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978).
29
 
30
  **Note:** `dorsal_images_cuthill` contains processed dorsal images from the original Cuthill dataset (all 1,234 specimens).
31
 
 
45
 
46
  ### Supported Tasks and Leaderboards
47
 
48
+ _Heliconius erato_ and _Heliconius melpomene_ subspecies identification (image classification), with variable settings for acuity of the observer (bird, butterfly, or human/other).
49
 
50
  ### Languages
51
 
 
120
  * Background: [210, 210, 210] (gray)
121
  * Fit in frame: Most padding is above and below the image, some on the left and right.
122
  * Ruler or Scale: None
123
+ * Color Reference (ColorChecker, white-balance, None): None
124
 
125
 
126
  ### Data Fields
 
134
  * `Subspecies`: subspecies of the specimen
135
  * `Sex`: sex of the specimen (male or female)
136
  * `addit_taxa_info`: additional taxonomic information (subspecies)
137
+ * `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.
138
  * `hybrid_stat`: hybrid status ('valid subspecies', 'subspecies synonym' or 'unknown' (only 1))
139
+ * `in_reduced`: whether or not the specimen was used in the second analysis by 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.
140
  * `locality`: where specimen was collected
141
  * `lat`: latitude where specimen was collected
142
  * `lon`: longitude where specimen was collected
143
  * `speciesdesig`: species designation, first initial of species '.' subspecies (eg., 'm. rosina')
144
 
145
  `Train_Test_Curated_GoldStandard_Hoyal_Cuthill.csv` has three additional columns:
146
+ * `Image_filename_png`: filename of (png) image of specimen, `dorsal_images_cuthill/ + <Image_filename_png>` is the filepath for the processed dorsal image
147
  * `subset`: whether this is part of the training or test set (`train` or `test`)
148
  * `filepath`: the filepath for the train or test image
149
 
 
175
  ### Curation Rationale
176
 
177
  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).
178
+ The original data (Cuthill et al. 2019) had misclassified species/subspecies and some locality/ collection sites were outside the known range of the butterflies.
179
  It also contained hybrid and aberrant samples, that had the potential to muddle classification results.
180
  To prevent this, the data was further refined by several Heliconius experts to remove hybrid and aberrant samples.
181
  Lastly, bird and butterfly acuities were added to provide another level of analysis.
 
183
 
184
  ### Source Data
185
 
186
+ Cuthill et al. [doi:10.5061/dryad.2hp1978](https://doi.org/10.5061/dryad.2hp1978).
187
 
188
  #### Initial Data Collection and Normalization
189
 
 
190
  Photographers: Robyn Crowther and Sophie Ledger, Natural History Museum, London.
191
 
192
  #### Who are the source language producers?
 
197
 
198
  #### Annotation process
199
 
200
+ 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.
201
+ Some localities were outside the known range of the butterflies, and were removed using QGIS and known subspecies ranges.
202
 
203
  #### Who are the annotators?
204
 
205
+ Christopher Lawrence,
206
+ Jim Mallet,
207
+ Owen McMilan, and
208
+ Krzysztof Kozak.
209
 
210
  ### Personal and Sensitive Information
211
 
 
219
 
220
  ### Discussion of Biases
221
 
222
+ Biased towards species and subspecies within Heliconius. Focused on _Heliconius erato_ and _Heliconius melpomene_.
223
 
224
  ### Other Known Limitations
225
 
 
247
 
248
  ### Licensing Information
249
 
250
+ 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/).
251
 
252
  ### Citation Information
253
 
 
255
 
256
  Please also cite the original dataset from which this was adapted and its accompanying paper:
257
  * 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.
258
+ * 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.
259
 
260
  ### Contributions
261
 
262
+ 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).