Home
Welcome to the MoSeq2 Wiki! The documentation should reflect the latest version of MoSeq2. If it does not, please submit an issue describing where the documentation needs updating. Please join our Slack channel! Once you join you'll be able to talk to the MoSeq team directly for help or information and talk to other community members about how you use MoSeq.
Start here to learn more about how to use MoSeq for your experiments. Please read through these guides before setting up MoSeq to gain familiarity with the pipeline. Use the sidebar to navigate through the different topics related to MoSeq. You can find a nice high-level overview of MoSeq in our README. This wiki contains guides for:
- Hardware setup for data acquisition
- Documentation for data acquisition
- Steps for MoSeq2 installation
- Guides for running the MoSeq2 pipeline
Many of MoSeq's interactive features require using a Jupyter notebook or JupyterLab. Please take some time to get familiar with these tools.
Read below for an overview of MoSeq2's documentation. You can find links for navigating the wiki in the sidebar too.
Head to the experiment setup page for links to
- the bill of materials for the acquisition cage
- installation instructions
- recording bucket preparation
Click the following link for instructions on how to use the acquisition software with the Kinect v2.
Although we don't currently support the newest Microsoft depth sensor, the Azure Kinect, we plan to support it in the future. Follow updates on the documentation here:
There are 3 options for using MoSeq:
- Google Colab (for trying out and exploring MoSeq)
- Docker (recommended installation route)
- Anaconda (recommended for experienced python users or HPC/SLURM users)
Pick out the option that is most suitible for your needs. However, we strongly urge first-time users to install MoSeq2 via Docker. You can also find this information on the MoSeq2 installation page.
This option is preferrable for people just looking to play with MoSeq and get a feel for the pipeline. The colab notebooks are set up with some test data so that you can explore how data extraction and processing work. Click the button above or follow this link to get started.
We strongly suggest this option for people new to using the terminal or new to programming. Docker runs virtual containers with MoSeq2 pre-installed. This means that once Docker is installed and you download the MoSeq2 Docker image, you'll be able to start using MoSeq2 immediately. Use the following links for platform-specific installation steps:
We recommend the Anaconda installation route for users who have more experience with the command line, python, and virtual environments or users using a high-performance computing cluster. This installation route uses the Anaconda environment and package manager to install a MoSeq2 environment. Users have more flexibility with this method. Links for platform-specific installation steps found here:
After successfully installing MoSeq2, head on over to the pipeline documentation to get familiar with the two main components of the MoSeq2 pipeline:
- extraction and modeling: via Jupyter notebooks or the command line interface
- analysis: via Jupyter notebooks or the command line interface
Other tutorials:
Resources:
Latest versions
moseq2-extract==1.0.1betamoseq2-pca==1.0.1betamoseq2-model==1.0.1betamoseq2-viz==1.0.2betamoseq2-app==1.0.2beta
MoSeq2 logo by Sigrid Knemeyer
Updated 12/23/2021.
Home | Changelog | Acquisition | Installation | Analysis Pipeline | Troubleshooting and Tips |
Tutorials |
Join our slack