diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 000000000..9bc9e6c39 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +*.ipynb \ No newline at end of file diff --git a/examples/distance_task/liver_peroxisome.ipynb b/examples/distance_task/liver_peroxisome.ipynb index 8a455d522..b38c0e7a8 100644 --- a/examples/distance_task/liver_peroxisome.ipynb +++ b/examples/distance_task/liver_peroxisome.ipynb @@ -21,6 +21,35 @@ "These are then combined in a single **dacapo.experiments.Run** that includes your starting point (whether you want to start training from scratch or continue off of a previously trained model) and stopping criterion (the number of iterations you want to train)." ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Environment setup\n", + "If you have not already done so, you will need to install DaCapo. You can do this by first creating a new environment and then installing DaCapo using pip.\n", + "\n", + "```bash\n", + "conda create -n dacapo python=3.10\n", + "conda activate dacapo\n", + "```\n", + "\n", + "Then, you can install DaCapo using pip, via GitHub:\n", + "\n", + "```bash\n", + "pip install git+https://github.com/janelia-cellmap/dacapo.git\n", + "```\n", + "\n", + "Or you can clone the repository and install it locally:\n", + "\n", + "```bash\n", + "git clone https://github.com/janelia-cellmap/dacapo.git\n", + "cd dacapo\n", + "pip install -e .\n", + "```\n", + "\n", + "Be sure to select this environment in your Jupyter notebook or JupyterLab." + ] + }, { "cell_type": "markdown", "metadata": {}, diff --git a/examples/distance_task/liver_peroxisome.md b/examples/distance_task/liver_peroxisome.md index 78ff3cf24..734b9c998 100644 --- a/examples/distance_task/liver_peroxisome.md +++ b/examples/distance_task/liver_peroxisome.md @@ -13,6 +13,29 @@ DaCapo has 4 major configurable components: These are then combined in a single **dacapo.experiments.Run** that includes your starting point (whether you want to start training from scratch or continue off of a previously trained model) and stopping criterion (the number of iterations you want to train). +## Environment setup +If you have not already done so, you will need to install DaCapo. We recommend you do this by first creating a new environment and then installing DaCapo using pip. + +```bash +conda create -n dacapo python=3.10 +conda activate dacapo +``` + +Then, you can install DaCapo using pip, via GitHub: + +```bash +pip install git+https://github.com/janelia-cellmap/dacapo.git +``` + +Or you can clone the repository and install it locally: + +```bash +git clone https://github.com/janelia-cellmap/dacapo.git +cd dacapo +pip install -e . +``` + + ## Config Store To define where the data goes, create a dacapo.yaml configuration file. Here is a template: diff --git a/setup.py b/setup.py index 3e6f51064..ed7503f1c 100644 --- a/setup.py +++ b/setup.py @@ -41,5 +41,7 @@ "cattrs", "numpy-indexed", "click", + "ipykernel", + "jupyter", ], )