It's a single-plane, single-channel recording. zip files for these two parts can be downloaded from these links: test_inputs and test_outputs.Īn example dataset is provided here. The test data is split into two parts: test inputs and expected test outputs which will be downloaded in data/test_inputs and data/test_outputs respectively. Run tests: python setup.py test or pytest -vs, this will automatically download the test data into your suite2p folder.Install the local version of suite2p into this environment in develop mode with the command pip install -e.To activate this new environment, run conda activate suite2p (you will have to activate every time you want to run suite2p).Clone the repository and cd suite2p in an anaconda prompt / command prompt with conda for python 3 in the path.The registration step runs faster on Ubuntu than Windows, so if you have a choice we recommend using the Ubuntu OS. Please post an issue if you have installation problems. The software has been heavily tested on Windows 10 and Ubuntu 18.04, and less well tested on Mac OS. If you are on Yosemite Mac OS, PyQt doesn't work, and you won't be able to install suite2p. Clone the repository with git and cd suite2p.If you want to download and edit the code, and use that version, Installing the latest github version of the code Follow steps 4-7 in the installation section above to install the suite2p package.Use the following command CONDA_SUBDIR=osx-64 conda create -name suite2p python=3.8.Open up this iTerm app and follow steps 1 & 2 in the installation section above to install anaconda.Navigate to the iTerm app you will use, right click it, and then select "Get Info".If you already have downloaded iTerm, duplicate it and give it whatever name you'd like (e.g., "iterm2Rosetta"). Install it into your /Applications folder. Download an iTerm2 terminal from this link.Installation for Macs with Apple Silicon chips (e.g., M1) To upgrade the suite2p (package here), run the following in the environment: pip install -upgrade suite2p If you want to run jupyter notebooks in this environment, then also conda install jupyter. Conda ensures mkl_fft and numba run correctly and quickly on your machine. Note you will always have to run conda activate suite2p before you run suite2p. If you have an older suite2p environment you can remove it with conda env remove -n suite2p before creating a new one. Running the command suite2p -version in the terminal will print the install version of suite2p.Now run python -m suite2p and you're all set.If you're on a zsh server, you may need to use ' ' around the suite2p call: python -m pip install 'suite2p'. (Option 2) You can install the GUI version with python -m pip install suite2p.(Option 1) You can install the minimal version of suite2p, run python -m pip install suite2p.To activate this new environment, run conda activate suite2p.Create a new environment with conda create -name suite2p python=3.8.Open an anaconda prompt / command prompt with conda for python 3 in the path. Note you might need to use an anaconda prompt if you did not add anaconda to the path. Install an Anaconda distribution of Python - Choose Python 3.8 and your operating system.Read the Documentation at Installation Installation for Linux, Windows, and MacOS (intel processors) machines Suite2p: beyond 10,000 neurons with standard two-photon microscopy. Pachitariu, M., Stringer, C., Schröder, S., Dipoppa, M., Rossi, L. If you use this package in your research, please cite the paper: Lectures on how suite2p works are available here. Note that the algorithm is older and will not work as well on non-circular ROIs. See this twitter thread for GUI demonstrations. Note you do not have access to the GUI via google colab, but you can download the processed files and view them locally in the GUI. You can now run suite2p in google colab, no need to locally install. The deconvolution algorithm is based on this paper, with settings based on this paper. This code was written by Carsen Stringer and Marius Pachitariu. Pipeline for processing two-photon calcium imaging data.Ĭopyright (C) 2018 Howard Hughes Medical Institute Janelia Research Campus
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