Download Test Data

We have curated 4 datasets so that you can try out MoSeq without your own data or, if you have your own data, compare your results with ours. They can be downloaded one of two ways:

1. through the download links (easiest, but downloading large files might spontaneously fail)
2. through bash scripts (requires more effort, but downloads are slightly more robust)

Datasets

Each of the datasets we provide contains two experimental cohorts with equal numbers of mice. One cohort was injected with amphetamine (2 mg/kg) while the other was injected with saline as a control. Each mouse was recorded using MoSeq2 for one 30-minute session. Our tutorials in this wiki focus on analyzing and distinguishing patterns of behavior unique to each experimental cohort.

• If you want to run the full MoSeq pipeline relatively quickly, download the small dataset.
• If you want to try our analysis and visualization tools without having to extract the data (extraction can take quite a long time), download the extraction + model results only.
• If you want to compare your experimental results/data with ours, download the full dataset or full dataset + extraction.

1. Download links

Click any of the links below to download a zip file with the example data we provide. Once the zip file is downloaded, decompress the file. A folder should appear containing folders for raw depth recordings if they are present and/or folders and files for extractions, PCA, and models. See Directory Structures and yaml Files in MoSeq Pipeline for more information about how data is organized for MoSeq.

• small dataset (20 raw depth recordings; zip file 27.9GB, uncompressed 30.2GB)
  • approximate download time: 6-13 minutes (assuming an internet speed of 300-800Mb/s)
• extraction + model results only (48 extractions + PCA results + model results; zip file 2.0GB, uncompressed 2.6GB)
  • approximate download time: 1-2 minutes
• full dataset (48 raw depth recordings; zip file 67.2GB, uncompressed 72.7GB)
  • approximate download time: 12-31 minutes
• full dataset + extraction (48 raw depth recordings + extractions + PCA results + model results zip file 71GB, uncompressed 77.8GB)
  • approximate download time: 13-33 minutes

2. bash scripts

Note: If you are on WSL2 or Linux (Ubuntu/Debian), you might need to install the unzip package before you run the download scripts:

sudo apt install unzip

Small Dataset

The small dataset contains 20 sessions of 30-minute depth videos. In 10 of the sessions, the mice are injected with amphetamine and in the other 10 sessions, the mice are injected with saline.

You can download the small dataset using this download script. This script is also available in the scripts folder in the moseq2-app folder when you clone the repository. Put the script in your desired location where you want to store the test data. In your Terminal, navigate to the directory where you want to keep the test data using cd (eg. cd ./Desktop). Then run:

<directory that has moseq2-app>/moseq2-app/scripts/download_small_dataset.sh

If moseq2-app is in the same directory as the one you want to keep the test data (eg. Desktop), after running cd Desktop, run the following command to download the data:

./moseq2-app/scripts/download_small_dataset.sh

Full Dataset

The full dataset contains 48 sessions of 30-minute depth videos. In 24 of the sessions, the mice are injected with amphetamine and in the other 24 sessions, the mice are injected with saline.

You can download the full dataset using this download script. This script is also available in the scripts folder in the moseq2-app folder when you clone the repository. Put the script in your desired location where you want to store the test data. In your Terminal, navigate to the directory where you want to keep the test data using cd (eg. cd ./Desktop). Then run:

<directory that has moseq2-app>/moseq2-app/scripts/download_full_dataset.sh

If moseq2-app is in the same directory as the one you want to keep the test data (eg. Desktop), after running cd Desktop, run the following command to download the data:

./moseq2-app/scripts/download_full_dataset.sh

Full Dataset + Extraction

The extracted full dataset contains the same 48 sessions as the full dataset. Processing depth videos, extracting the regions of interest, and running the model could be resource-intensive and time-consuming so this dataset contains pre-extracted and pre-computed models for users to explore the interactive results widgets.

You can download the extracted full dataset using this download script. This script is also available in the scripts folder in the moseq2-app folder when you clone the repository. Put the script in your desired location where you want to store the test data. In your Terminal, navigate to the directory where you want to keep the test data using cd (eg. cd ./Desktop). Then run:

<directory that has moseq2-app>/moseq2-app/scripts/download_extracted_full_dataset.sh

If moseq2-app is in the same directory as the one you want to keep the test data (eg. Desktop), after running cd Desktop, run the following command to download the data:

./moseq2-app/scripts/download_extracted_full_dataset.sh

Extraction + Model Results Only

The extracted full dataset contains the same 48 sessions as the full dataset but the raw depth videos are not included. This dataset doesn't include the raw depth videos so it is much smaller. Processing depth videos, extracting the regions of interest, and running the model could be resource-intensive and time-consuming so this dataset contains pre-extracted and pre-computed models for users to explore the interactive results widgets in the Analysis Visualization notebook.

You can download the extracted full dataset using this download script. This script is also available in the scripts folder in the moseq2-app folder when you clone the repository. Put the script in your desired location where you want to store the test data. In your Terminal, navigate to the directory where you want to keep the test data using cd (eg. cd ./Desktop). Then run:

<directory that has moseq2-app>/moseq2-app/scripts/download_extracted_model_results.sh

If moseq2-app is in the same directory as the one you want to keep the test data (eg. Desktop), after running cd Desktop, run the following command to download the data:

./moseq2-app/scripts/download_extracted_model_results.sh

Good Extraction and Bad Extraction Example Sessions

We have provided 2 short testing sessions to exemplify what a good versus bad extraction looks like.

• An example of a good recording
• a bad example recording