Big-FISH¶
Getting started¶
To avoid dependency conflicts, we recommend the the use of a dedicated virtual or conda environment. In a terminal run the command:
$ conda create -n bigfish_env python=3.6
$ source activate bigfish_env
We recommend two options to then install Big-FISH in your virtual environment.
Download the package from PyPi¶
Use the package manager pip to install Big-FISH. In a terminal run the command:
$ pip install big-fish
Clone package from Github¶
Clone the project’s Github repository and install it manually with the following commands:
$ git clone git@github.com:fish-quant/big-fish.git
$ cd big-fish
$ pip install .
Examples¶
Several examples are available as Jupyter notebooks:
Read and write images.
Normalize and filter images.
Project in two dimensions.
Segment nuclei and cells.
Detect spots.
Extract cell level results.
Analyze coordinates.
You can also run these example online with mybinder. The remote server can take a bit of time to start.
API reference¶
Support¶
If you have any question relative to the package, please open an issue on Github.