Installation#

Prerequisites#

Before installing Phenotypic, ensure you have the following prerequisites:

Python 3.10 or higher
pip (Python package installer)
uv (recommended; see https://docs.astral.sh/uv/)

Installation Methods#

From PyPi#

Using uv (recommended)#

uv add phenotypic

Using pip#

pip install phenotypic

From Source#

To install from source:

git clone https://github.com/exfab/PhenoTypic.git
cd PhenoTypic && uv sync

Optional Extras#

PhenoTypic provides optional extras for different use cases:

[gui] — Full interactive environment including napari viewer, Panel dashboards, and Jupyter integration. Required for image.rgb.napari() and related viewer methods.
[torch] — PyTorch + SAM2 for Sam2Detector (Linux/macOS only).

# Full interactive / GUI environment (napari, Panel, Jupyter)
uv add "phenotypic[gui]"

# SAM2 GPU detector (Linux/macOS)
uv add "phenotypic[torch]"

micro_sam (used by MicroSamDetector) is only published on conda-forge and is not included in any PhenoTypic extra. See the GPU Detection Setup guide for a self-service recipe that combines PhenoTypic and micro_sam in a single pixi environment.

Development Installation#

For development of new modules, sync with the dev (and optionally docs) dependency groups:

git clone https://github.com/exfab/PhenoTypic.git
cd PhenoTypic
uv sync --group dev --group docs

Verification#

To verify the installation, run:

import phenotypic
print(phenotypic.__version__)