Kilosort4 image

Author: alejoe91

kilosort4/Dockerfile

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+FROM nvidia/cuda:12.0.0-base-ubuntu20.04
+
+LABEL maintainer="Alessio Buccino <alessiop.buccino@gmail.com>"
+
+# USER root
+# Ubuntu package installs
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    libfftw3-dev \
+    git \
+    wget && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# install miniconda
+ENV MINICONDA_VERSION 24.1.2-0
+ENV PY_VERSION py311
+ENV CONDA_DIR /home/miniconda3
+ENV LATEST_CONDA_SCRIPT "Miniconda3-${PY_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"
+
+RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
+    bash ~/miniconda.sh -b -p $CONDA_DIR && \
+    rm ~/miniconda.sh
+ENV PATH=$CONDA_DIR/bin:$PATH
+RUN conda update conda && \
+    conda install conda-build
+
+# make conda activate command available from /bin/bash --login shells
+RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> /root/.profile 
+# make conda activate command available from /bin/bash --interactive shells
+RUN conda init bash
+
+# install torch
+# RUN conda install -y pytorch pytorch-cuda=11.8 -c pytorch -c nvidia
+RUN pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
+
+# install kilosort4
+RUN git clone https://github.com/MouseLand/Kilosort.git && \
+    cd Kilosort && \
+    pip install . && \
+    cd ..

kilosort4/README.md

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+### Build this image
+Build default image: 
+docker build -t pykilosort:latest -f dockerfiles/Dockerfile .
+
+Build image with additional testing components: 
+docker build -t pykilosort:test -f dockerfiles/Dockerfile.testing context
+
+### Run container
+docker run --rm -it -v <host-data-folder>:<docker-data-folder> --gpus all pykilosort:latest
+flags:
+--rm: removes container once it's stopped
+-it: for interactive session
+-v: mounted volumes (directories)
+--gpus: enables GPU use within container 
+
+### Test
+Download Neuropixel 1.0 data to your data directory: https://catalystneuro.github.io/spike-sorting-hackathon/datasets/datasets.html#allen-institute-example
+(see also https://github.com/int-brain-lab/pykilosort/tree/ibl_prod/examples, although apparently not up to date)
+
+$docker run --rm -it -v /my/dir/to/data:/data --gpus all pykilosort
+#conda activate pyks2
+#cd /data
+    --- alternatively, get data from kachery (if installed and configured) ---
+    ```
+    wget https://catalystneuro.github.io/spike-sorting-hackathon/datasets/examples/example_allen_NP1.py
+    python example_allen_NP1.py
+    ```
+
+The either run tests in ipython console, or run example from /home/test_file directory (if using `.testing` image), after editing directory paths
+#ipython
+```
+from pathlib import Path
+from pykilosort import run, add_default_handler, np1_probe, np2_probe
+
+data_path = Path('/data/Allen_Institute_NP1/continuous_1min.bin')
+dir_path = Path('/data/Allen_Institute_NP1/output')
+add_default_handler(level='INFO') # print output as the algorithm runs
+run(data_path, dir_path=dir_path, probe=np1_probe(sync_channel=False))
+```

kilosort4/build.sh

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+#!/bin/bash
+
+docker build -t spikeinterface/kilosort4-base:latest -t spikeinterface/kilosort4-base:0.1.0 .

kilosort4/push.sh

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+#!/bin/bash
+
+docker push --all-tags spikeinterface/kilosort4-base