Online collection of my conda environments. Kept here for consistency across computers.

Without vim

By default the enviroments will not have jupyterlab-vim and jupyterlab-vimrc installed. To install these add vim to the file name the just before the yaml. e.g. jupyter.yaml -> jupyter-vim.yaml

Choose your own environment name

The environments come with default names, however you can use the --name flag to override that and use your own name. e.g. mamba env create --force [...] --name <YOUR ENV NAME>

General Usage

jupyter

Good setup for generic analysis. Contains numpy matplotlib etc and jupyterlab with interactive matplotlib, a nice dark theme and vim extensions.

mamba env create --force --file https://hekstra-lab.github.io/envs/envs/jupyter.yaml

Microscopy

Everything here is based on jupyter and also contains xarray

micro-base

base env + napari + xarray + image loading

mamba env create --force --file https://hekstra-lab.github.io/envs/envs/micro-base.yaml

micro-analysis

micro-base + scikit image and learn

mamba env create --force --file https://hekstra-lab.github.io/envs/envs/micro-analysis.yaml

micro-control

micro-base plus Controlling microscopes with pymmcore-plus and napari-micromanager

mamba env create --force --file https://hekstra-lab.github.io/envs/envs/micro-control.yaml