README.md

---
task_categories:
- image-classification
tags:
- butterfly
- heliconius
- dorsal
- ventral
- RGB
- full body
- separated wings
- mimicry
- CV
pretty_name: Jiggins Heliconius Collection
size_categories:
- 10K<n<100K
language:
- en
---
# Dataset Card for Jiggins Heliconius Collection

## Dataset Description

- **Homepage:** 
- **Repository:** 
- **Paper:** 
- **Leaderboard:** 
- **Point of Contact:** 

### Dataset Summary

Subset of the collection records from the research group of Chris Jiggins at the University of Cambridge derived from almost 20 years of field studies. 
This subset contains approximately 49,359 RGB images of 12,586 specimens (34,929 images of 9,546 specimens across all Heliconius). Many records include images as well as locality data. 
All detached wings were photographed with a DSLR camera with a 100 mm macro-lens in standardized conditions; images and full records with data are stored in the [EarthCape database](https://heliconius.ecdb.io/default.aspx) and on [Zenodo](https://zenodo.org/communities/butterfly?q=&l=list&p=1&s=10&sort=newest) (across 32 records from the Butterfly Genetics Group).

Both dorsal and ventral images available. Contains both whole butterfly, and 4 wings separate. Large variation in image content.

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This dataset card aims to be a base template for new datasets. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1).
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### Supported Tasks and Leaderboards

[More Information Needed]

### Languages

[More Information Needed]

## Dataset Structure

* **Jiggins_Zenodo_Img_Master.csv:** Information for the approximately 49,0000 unprocessed image files included in the Jiggins Heliconius Collection. Image types are `jpg`, `raw` (.CR2) and `tif`. `genus`, `species`, and `subspecies` are included columns.
     * To access the images combine columns `zenodo_link` and `Image_name`:
       ```
       zenodo_link + '/files/' + Image_name
       ```

* **Jiggins_Zenodo_dorsal_Img_Master.csv:** Subset of 24,318 images from `Jiggins_Zenodo_Img_Master.csv` with a dorsal view of the butterflies (note that some have both dorsal and ventral). This subset includes 12,296 unique specimens. Accessing the images from Zenodo works the same as above, and image types are `jpg`, `raw` (.CR2) and `tif`.

* **Jiggins_Heliconius_Master.csv:** The 34,929-image subset of all Heliconius images from `Jiggins_Zenodo_Img_Master.csv`. This subset includes 9,546 unique specimens. Accessing the images from Zenodo works the same as above, and image types are `jpg`, `raw` (.CR2) and `tif`. `species` and `subspecies` columns are also included.



* Note: The notebooks that generated these files and stats are included in the `notebooks` folder.


### Data Instances

`Jiggins_Heliconius_Master.csv` contains multiple species of Heliconius (including erato and melpomene), most are labeled down to the subspecies level. The `Jiggins_Zenodo_Img_Master.csv` also contains species from other genera, with just over half labeled to the subspecies level (these are predominantly Heliconius subspecies).
Detached wings in four quadrants (generally).
Some subspecies may be photographed differently, needs segmentation preprocessing.

* **Type:** JPG/jpg/tif(very few)
* **Size (x pixels by y pixels):** Unknown yet
* **Background (color or none):** multiple (needs to be normalized)
* **Fit in frame:**
* **Ruler or Scale:** Some with Ruler
* **Color (ColorChecker, white-balance, None):** None

#### Preprocessing steps (to be done):
1. Hybrid separation - some images labeled as _H. erato_ and _H. melpomene_ without subspecies names are hybrids and need to be determined what subspecies they are.
2. Label correction - along with step 1.
3. Removal of subspecies with no mimic pairs.
4. Segmentation of four wings from images so we can focus on forewings vs hindwings: [WingSeg](https://github.com/agporto/WingSeg).

Current preprocessing steps: [WingSeg](https://github.com/agporto/WingSeg) on the [Meier subset](https://huggingface.co/datasets/imageomics/Meier-Subset-Jiggins/).

### Data Fields

CSV Columns are as follows:

- `CAMID`: Unique identifier for each specimen that was photographed. Each `CAMID` corresponds to multiple images (based on factors such as `View` and `file_type`).
- `X`: Unique identifier for each line in the master CSV.
- `Image_name`: Filename of image.
- `View`: View of the butterfly in the image: `dorsal`, `ventral`, `forewing dorsal`, `hindwing dorsal`, `forewing ventral`, `hindwing ventral`, `dorsal and ventral`.
- `zenodo_name`: Name of the CSV file with metadata used to populate this file from the associated Zenodo record.
- `zenodo_link`: URL for the Zenodo record of the image.
- `Sequence`: Mostly numeric IDs, not unique, please see the associated Zenodo record for more information on the meaning of these designations.
- `Taxonomic_Name`: Indication of the Genus, Species, and possibly, subspecies, of the specimen. For Cross Types, this is just the Genus species pair (all _Heliconius erato_ or _Heliconius melpomene_).
- `Locality`: Likely location of specimen collection, varying levels of specificity. Please see the associated Zenodo record for more information on the meaning of these designations.
- `Sample_accession`: Some type of ID, not unique, please see the associated Zenodo record for more information on the meaning of these designations.
- `Collected_by`: Abbreviations (likely for those collecting the specimen), please see the associated Zenodo record for more information on the meaning of these designations.
- `Other_ID`: Mostly numeric IDs, not unique, please see the associated Zenodo record for more information on the meaning of these designations.
- `Date`: Please see the associated Zenodo record for more information on the meaning of these designations.
- `Dataset`: Overall collection the images belong to: `Heliconiine Butterfly Collection Records from University of Cambridge` (largely, but not entirely Heliconius), `Patricio Salazar`, `Nadeau Sheffield`, `Bogota Collection (Camilo Salazar)`, `Cambridge Collection`, `Mallet`, `Merril_Gamboa`, `STRI Collection (Owen)`. Please see the associated Zenodo record for more information on the meaning of these designations.
- `Store`: Storage location for specimen (`Box ###`).
- `Brood`: Likely indicator of batch of butterflies. Please see the associated Zenodo record for more information on the meaning of these designations.
- `Death_Date`: Date of specimen death. Only noted for 318 images.
- `Cross_Type`: Laboratory cross breeding information. There is a mix of F1 (subspecies x subspecies), F2 (F1 x F1), and backcross (F1 x subspecies) hybrids. Generally, the order of the subspecies listed in the cross corresponds to the sexes of the parents (Maternal x Paternal). There are approximately 5,000 such images; on average, there are both raw and jpg images of the specimens for each view, so this covers 820 unique specimens.
- `Stage`: Life stage of the specimen. Only 15 specimens have a non-null value for this feature, and they are all labeled as `Adult`.
- `Sex`: Sex of the specimen: `Male`, `Female`, or `Unknown`.
- `Unit_Type`: Type of the specimen: `wild`, `reared`, `Mutant`, `Wild`, `e11`, or `e12`. Please see the associated Zenodo record for more information on the meaning of these designations. 
- `file_type`: Image type: `jpg`, `raw` (.CR2), or `tif`.
- `record_number`: The number associated with the Zenodo record that the image came from.
- `species`: Species of the specimen. There are 246 species represented in the full collection, 37 of these are species of Heliconius.
- `subspecies`: Subspecies of the specimen (where available, mostly labeled for Heliconius). There are 155 subspecies represented in the full collection, 110 of which are Heliconius subspecies.
- `genus`: Genus of the specimen. There are 94 unique genera represented in the full collection.

**Note:**
 - `Jiggins_Heliconius_Master.csv` has all but the `genus` column, since all images are Heliconius.
 - `Jiggins_Zenodo_dorsal_Img_Master.csv` does not have the last four columns, but they can be added easily with the appropriate functions in `notebooks/standardize_taxa.ipynb`. This file also has a column `CAM_dupe` indicating whether the `CAMID` has multiple images within this subset.

### Data Splits

[More Information Needed]
      
## Dataset Creation

### Curation Rationale

[More Information Needed]

### Source Data

These images are a subset of the [Butterfly Genetics Group's Cambridge butterfly collection](https://zenodo.org/communities/butterfly?q=&f=subject%3ACambridge&l=list&p=1&s=10&sort=newest). This collection of butterfly images comes from the research group of Chris Jiggins at the University of Cambridge derived from almost 20 years of field studies.

Data is pulled from the Zenodo Records in [`licenses.json`](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/licenses.json). This file also contains full citation information for all records.

#### Initial Data Collection and Normalization

[More Information Needed]

#### Who are the source language producers?

[More Information Needed]

### Annotations

#### Annotation process

[More Information Needed]

#### Who are the annotators?

[More Information Needed]

### Personal and Sensitive Information

None

## Considerations for Using the Data

### Social Impact of Dataset

[More Information Needed]

### Discussion of Biases

[More Information Needed]

### Other Known Limitations

[More Information Needed]

## Additional Information

### Dataset Curators

* Christopher Lawrence (Princeton University) - ORCID: 0000-0002-3846-5968
* Chris Jiggins (University of Cambridge) - ORCID: 0000-0002-7809-062X
* Butterfly Genetics Group (University of Cambridge)

### Licensing Information

The data (images and text) are all licensed under [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/). Each image and text in this dataset is provided under the least restrictive terms allowed by its licensing requirements as provided to us (i.e, we impose no additional restrictions past those specified by this license on the original source files). Modified images are only restricted by this original license.

Images can be matched to their source record through the `zenodo_link` column in the Master CSVs to the `url` in the licenses.json file.

### Citation Information

Christopher Lawrence, Chris Jiggins, Butterfly Genetics Group (University of Cambridge). (2023). Jiggins Heliconius Collection. Hugging Face. https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection.

If you use this dataset, please cite the original datasets (citations for all 32 Zenodo records are in licenses.json) as well as this curated subset. 

### 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).