ToFScope

Explore, visualize, and analyze FIB ToF-SIMS data.

Links

View on PyPI

AI / Agents

llms.txt
llms-full.txt

Developers

Josh Taillon

Author

datasophos LLC

Community

Full license MIT

Meta

Requires: Python >=3.11
Package Info

ToFScope is a local, browser-based application for exploring time-of-flight secondary ion mass spectrometry (ToF-SIMS) data. It allows you to compare mass spectra, ion images, and depth profiles, inspect peaks, and explore signals in three dimensions.

Explore shows an ion image, mass spectrum, front projection, and depth profile together.

Quick Start

ToFScope can be easily installed from PyPI using uv:

uv tool install tofscope

That command will put the tofscope executable on your path. Run tofscope to launch the application. By default, ToFScope will only have access to whatever files are in the folder that you launch it from (or any subfolders). You can use the --data-root argument to allow read-only access to another folder (such as a network mount containing your instruments’ data) and the --output-root argument to allow for saving analysis results to a separate folder. For example:

tofscope --data-root /path/to/acquisitions --output-root /path/to/saved-analyses

When running in this manner, the ToFScope process will run in the terminal and then open the main interface in your default browser (similar to how Jupyter operates). For more detail, see:

• Install and launch: requirements, folder setup, and starting the app.
• Your first analysis: opening a file, comparing signals, and saving your work.
• Troubleshooting: help with startup, file access, and saving.

Feature Guides

What you want to do	Where to start
Exploring an acquisition and comparing ion signals	Signals and views
Relating acquisition frames to measured depth	Depth calibration
Comparing peaks with isotope candidates	Peak identification
Viewing the spatial distribution of signals	3D visualization
Sharing results or resuming an analysis	Saving and exports
Understanding the frontend, backend, and files	ToFScope architecture

For developers and administrators

The developer and administrator guides cover configuration, deployment, building and testing, and maintaining this site.

ToFScope supports TOFWERK TOFexplorer¹ HDF5 acquisitions. The file compatibility and limitations guide describes supported workflows and current validation boundaries.

Footnotes

1. TOFWERK and TOFexplorer are names owned by TOFWERK AG. ToFScope is an independent project and is not affiliated with, endorsed by, or sponsored by TOFWERK AG.