Installation

Requirements

cellfinder should run on most machines, but for routine use on large datasets, you will need a fairly high-powered computer (see the guide to Speeding up cellfinder for details).

Using an NVIDIA GPU will speed up cell classification considerably. See setting up your GPU for details.

To use cellfinder, you will need to have Python on your machine. Your machine may already have Python installed, but we recommend installing miniconda. See Using conda for details.

Installing the cellfinder package

You can use pip from inside your activated Python environment to install the cellfinder package directly. Make sure to install version 1.0.0 or later!

pip install cellfinder # Run this if you only want the Python API (for use in scripts)
pip install cellfinder[napari] # Run this if you want to install the API and the napari plugin

Downloading pre-trained models

If you would like to download the pre-trained models in advance (otherwise they will download as needed), please see Downloading the pre-trained model in advance.

Installing brainmapper

The brainmapper workflow combines the cellfinder and brainreg packages into a single workflow, providing full-brain registration and cell detection in one command. You can read more about it on this page.