SMAPpy is software for single-molecule localization microscopy (SMLM) in Python. It takes raw camera frames to localizations and super-resolution images, with a graphical interface, command-line tools and a Python API. It is a Python port of SMAP.
pip install smappy-smlm
The GUI is included. Binary wheels are available for Python 3.12-3.14 on macOS,
Linux and Windows, so nothing needs to be compiled. The package is called
smappy-smlm on PyPI; in Python you import smappy.
I need more help. Never used a terminal or pip?
Installing SMAPpy, step by step walks through
it on a Mac or Windows computer, from opening the terminal to starting the GUI,
and says what to ask an AI assistant that can do it for you.
With uv you can install the GUI as a standalone tool, or run it without installing:
uv tool install smappy-smlm
uvx --from smappy-smlm smappy-gui
To install from a checkout, which builds the C++ extensions (pip 21.3 or newer):
git clone https://github.com/ries-lab/SMAPpy.git
cd SMAPpy
python -m venv .venv
.venv/bin/python -m pip install -e .
smappy-gui
or, to open a localization file directly:
smappy-gui FILE.hdf5
Files can also be dropped onto either window: a localization file opens as
with File → Open; a short TIFF (50 frames or fewer) or a PNG is added as an
image layer, as with File → Open image; and a longer stack (TIFF, an NDTiff
folder, *.sim.yaml) becomes the file of the fitter on the Localize tab,
ready to fit.
From a checkout, activate the venv first or run .venv/bin/smappy-gui.
Tutorials. ries-lab.github.io/SMAPpy has short guided tours on simulated data you can follow along with. Start with SMAPpy in three minutes.
Help pages. Every plugin and the main parts of the GUI have a help page.
It explains the theoretical background and every control. Open it with the
? in a plugin's or a Render-tab section's title bar, with F1 in any panel or
window, or from Help → Plugin documentation. The same pages are online at
ries-lab.github.io/SMAPpy/help, and
python -m smappy.docs -o DIR writes them as a static website.
Your own analysis. When no plugin measures what you need, make one: describe it to an AI assistant started in your plugin folder (Plugins → Show my plugin folder), or start from the example with Plugins → New plugin.... A file saved there appears under Plugins → User. The help page Your own plugins explains how.
For developers. GUI.md describes the architecture. docs/ holds design notes on the plugin system and individual algorithms. NOTES.md records design decisions and measurements.
SMAPpy is released under the BSD 3-Clause license; see LICENSE and THIRD_PARTY_NOTICES.md.