# Datasets

Here we provide a number of sample and benchmark datasets that can be used for experimenting with or extending SLEAP.

These datasets are all saved as `.pkg.slp` files, which are self-contained SLEAP labels together with embedded image data. See [Data structures](../notebooks/Data_structures.ipynb) for examples on how to work with SLEAP files.

For the full set of labeled datasets and trained models reported in the SLEAP paper ([Pereira et al., Nature Methods, 2022](https://www.nature.com/articles/s41592-022-01426-1)), please see the [OSF repository](https://osf.io/36har/).

!!! hint
    Need a quick testing clip? [Here's a video of a pair of mice in a standard home cage setting.](https://storage.googleapis.com/sleap-data/sandbox/sleap-mice-demo/mice.mp4)

---

## Summary

| Dataset | Animal | Nodes | Animals | Identity | Labels |
|---------|--------|-------|---------|----------|--------|
| [`fly32`](#fly32) | Fruit fly | 32 | 1 | ✘ | 1,500 |
| [`mice_of`](#mice_of) | Mice | 11 | 1-5 | ✘ | 2,950 |
| [`mice_hc`](#mice_hc) | Mice | 5 | 2 | ✘ | 2,948 |
| [`bees`](#bees) | Bumblebees | 21 | 2 | ✘ | 1,604 |
| [`flies13`](#flies13) | Fruit flies | 13 | 2 | ✔ | 4,000 |
| [`gerbils`](#gerbils) | Gerbils | 14 | 4 | ✔ | 1,588 |

---

## Single Animal

### `fly32`
![fly32](../assets/images/example.fly32.jpg)

| Name          | `fly32` |
|---------------|---------|
| Description   | Animal-centered movies of single fruit fly (*Drosophila melanogaster*) freely moving in an enclosed circular arena with backlight. Videos were recorded with a camera that followed animal, so all images are roughly centered. |
| Videos        | 59      |
| Image size    | 192 x 192 x 1 |
| FPS           | 100     |
| Resolution    | 35 px / mm |
| Skeleton      | 32 nodes |
| Num Animals   | 1       |
| Identity      | ✘       |
| Labels        | 1500    |
| Download      | [Train (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/BermanFlies/random_split1/train.pkg.slp) / [Validation (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/BermanFlies/random_split1/val.pkg.slp) / [Test (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/BermanFlies/random_split1/test.pkg.slp) |
| Example       | [Clip (`.mp4`)](https://storage.googleapis.com/sleap-data/datasets/BermanFlies/clips/072212_173836%400-3200.mp4) / [Tracking (`.slp`)](https://storage.googleapis.com/sleap-data/datasets/BermanFlies/clips/072212_173836%400-3200.slp) |
| Credit        | [Berman et al. (2014)](https://royalsocietypublishing.org/doi/10.1098/rsif.2014.0672), [Pereira et al. (2019)](https://www.nature.com/articles/s41592-018-0234-5), [Pereira et al. (2022)](https://www.nature.com/articles/s41592-022-01426-1), Talmo Pereira, Gordon Berman, Joshua Shaevitz |

---

## Multi-Animal (without identity)

### `mice_of`
![mice_of](../assets/images/example.mice_of.jpg)

| Name          | `mice_of` |
|---------------|-----------|
| Description   | Freely moving C57BL/6J mice (*Mus musculus*) in 45.7 x 45.7 cm open field arena with a clear acrylic floor, imaged from below to ensure paw visibility. |
| Videos        | 20        |
| Image size    | 1280 x 1024 x 1 |
| FPS           | 80        |
| Resolution    | 1.97 px / mm |
| Skeleton      | 11 nodes  |
| Num Animals   | 1-5       |
| Identity      | ✘         |
| Labels        | 1000 frames, 2950 instances |
| Download      | [Train (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/wang_4mice_john/labels.full/random_split1/train.pkg.slp) / [Validation (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/wang_4mice_john/labels.full/random_split1/val.pkg.slp) / [Test (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/wang_4mice_john/labels.full/random_split1/test.pkg.slp) |
| Example       | [Clip (`.mp4`)](https://storage.googleapis.com/sleap-data/datasets/wang_4mice_john/clips/OFTsocial5mice-0000-00%4015488-18736.mp4) / [Tracking (`.slp`)](https://storage.googleapis.com/sleap-data/datasets/wang_4mice_john/clips/OFTsocial5mice-0000-00%4015488-18736.slp) |
| Credit        | [Pereira et al. (2022)](https://www.nature.com/articles/s41592-022-01426-1), John D'Uva, Mikhail Kislin, Samuel S.-H. Wang |

### `mice_hc`
![mice_hc](../assets/images/example.mice_hc.jpg)

| Name          | `mice_hc` |
|---------------|-----------|
| Description   | Pairs of male and female white Swiss Webster mice (*Mus musuculus*) imaged in a home cage environment with lightly-colored bedding, imaged from above. Animals are fairly low contrast with respect to the background. |
| Videos        | 40        |
| Image size    | 1280 x 1024 x 1 |
| FPS           | 40        |
| Resolution    | 1.9 px / mm |
| Skeleton      | 5 nodes   |
| Num Animals   | 2         |
| Identity      | ✘         |
| Labels        | 1474 frames, 2948 instances |
| Download      | [Train (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/eleni_mice/random_split1/train.pkg.slp) / [Validation (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/eleni_mice/random_split1/val.pkg.slp) / [Test (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/eleni_mice/random_split1/test.pkg.slp) |
| Example       | [Clip (`.mp4`)](https://storage.googleapis.com/sleap-data/datasets/eleni_mice/clips/20200111_USVpairs_court1_M1_F1_top-01112020145828-0000%400-2560.mp4) / [Tracking (`.slp`)](https://storage.googleapis.com/sleap-data/datasets/eleni_mice/clips/20200111_USVpairs_court1_M1_F1_top-01112020145828-0000%400-2560.slp) |
| Credit        | [Pereira et al. (2022)](https://www.nature.com/articles/s41592-022-01426-1), Eleni Papadoyannis, Mala Murthy, Annegret Falkner |

### `bees`
![bees](../assets/images/example.bees.jpg)

| Name          | `bees`    |
|---------------|-----------|
| Description   | Pairs of female worker bumblebees (*Bombus impatiens*) freely interacting in a petri dish with hexagonal beeswax flooring for up to 30 minutes |
| Videos        | 18        |
| Image size    | 1536 x 2048 x 1 |
| FPS           | 100       |
| Resolution    | 14 px / mm |
| Skeleton      | 21 nodes  |
| Num Animals   | 2         |
| Identity      | ✘         |
| Labels        | 804 frames, 1604 instances |
| Download      | [Train (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/yan_bees/random_split1/train.pkg.slp) / [Validation (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/yan_bees/random_split1/val.pkg.slp) / [Test (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/yan_bees/random_split1/test.pkg.slp) |
| Example       | [Clip (`.mp4`)](https://storage.googleapis.com/sleap-data/datasets/yan_bees/clips/bees_demo%4021000-23000.mp4) / [Tracking (`.slp`)](https://storage.googleapis.com/sleap-data/datasets/yan_bees/clips/bees_demo%4021000-23000.slp) |
| Credit        | [Pereira et al. (2022)](https://www.nature.com/articles/s41592-022-01426-1), Grace McKenzie-Smith, Z. Yan Wang, Joshua Shaevitz, Sarah Kocher |

---

## Multi-Animal (with identity)

### `flies13`
![flies13](../assets/images/example.flies13.jpg)

| Name          | `flies13` |
|---------------|-----------|
| Description   | Freely interacting pairs of virgin male and female fruit flies (*Drosophila melanogaster*, NM91 strain) 3 to 5 days post-eclosion. Animals frequently engage in courtship behavior. |
| Videos        | 30        |
| Image size    | 1024 x 1024 x 1 |
| FPS           | 150       |
| Resolution    | 30.3 px / mm |
| Skeleton      | 13 nodes  |
| Num Animals   | 2         |
| Identity      | ✔         |
| Labels        | 2000 frames, 4000 instances |
| Download      | [Train (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/wt_gold.13pt/tracking_split2/train.pkg.slp) / [Validation (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/wt_gold.13pt/tracking_split2/val.pkg.slp) / [Test (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/wt_gold.13pt/tracking_split2/test.pkg.slp) |
| Example       | [Clip (`.mp4`)](https://storage.googleapis.com/sleap-data/datasets/wt_gold.13pt/clips/talk_title_slide%4013150-14500.mp4) / [Tracking (`.slp`)](https://storage.googleapis.com/sleap-data/datasets/wt_gold.13pt/clips/talk_title_slide%4013150-14500.slp) |
| Credit        | [Pereira et al. (2022)](https://www.nature.com/articles/s41592-022-01426-1), Junyu Li, Shruthi Ravindranath, Talmo Pereira, Mala Murthy |

### `gerbils`
![gerbils](../assets/images/example.gerbils.jpg)

| Name          | `gerbils` |
|---------------|-----------|
| Description   | Selected videos from a continuous monitoring setup of a home cage with 2 pup and 2 adult gerbils (*Meriones unguiculatus*), from P15 to 8 months old. Some animals are partially shaved to distinguish their appearance. |
| Videos        | 23        |
| Image size    | 1024 x 1280 x 3 |
| FPS           | 25        |
| Resolution    | 2 px / mm |
| Skeleton      | 14 nodes  |
| Num Animals   | 4         |
| Identity      | ✔         |
| Labels        | 425 frames, 1588 instances |
| Download      | [Train (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/nyu-gerbils/cohort1_compressedTalmo_23vids_march_7_to_march_17/random_split1.day001/train.pkg.slp) / [Validation (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/nyu-gerbils/cohort1_compressedTalmo_23vids_march_7_to_march_17/random_split1.day001/val.pkg.slp) / [Test (`.pkg.slp`)](https://storage.googleapis.com/sleap-data/datasets/nyu-gerbils/cohort1_compressedTalmo_23vids_march_7_to_march_17/random_split1.day001/test.pkg.slp) |
| Example       | [Clip (`.mp4`)](https://storage.googleapis.com/sleap-data/datasets/nyu-gerbils/clips/2020-3-10_daytime_5mins_compressedTalmo%403200-5760.mp4) / [Tracking (`.slp`)](https://storage.googleapis.com/sleap-data/datasets/nyu-gerbils/clips/2020-3-10_daytime_5mins_compressedTalmo%403200-5760.slp) |
| Credit        | [Pereira et al. (2022)](https://www.nature.com/articles/s41592-022-01426-1), Catalin Mitelut, Marielisa Diez Castro, Dan H. Sanes |