SciStudio user guide

Welcome. This guide lives inside your project so it is always at hand. It covers using SciStudio — building and running workflows, looking at your data, and writing your own blocks and plots — for people doing the science, not software engineers. If you can write a Python function, you can do everything here; and for most of it, you can simply ask the AI assistant.

Start here

New to SciStudio? Read getting-started.md — it takes you from choosing how to use SciStudio to your first run in five steps.

Want to work inside your AI app? Start with Using SciStudio in your AI app to connect through the app's built-in browser. For the assistant inside the SciStudio desktop window, follow Install a provider.

The guide

Using the app

Page	What it covers
getting-star ted.md	The five-minute tour: project → workflow → run → preview
Using SciStudio in your AI app	Start External AI mode, connect from an AI app, and manage the background service
how-scistudio-works.md	The short architecture map: data, blocks, lineage, AI agents, plots, and extensions
using-the-gui.md	The canvas in depth: building workflows, running them, previewing data
use-panels.md	The three kinds of panels: previews, interactive decisions, MiniApps
miniapps.md	Using MiniApps for data exploration and interaction
built-in-blocks.md	Every block that ships with SciStudio and what it does
history-and-branches.md	Go back to past work; keep pipeline variants on branches
ai-assistant.md	External AI apps, the desktop CLI assistant, and AI Agent blocks
learning-center.md	Guided tutorials and the in-app reading tab

Making your own

Page	What it covers
data-types.md	The data types that flow between blocks, and which one fits your data
writing-blocks.md	Write a custom block from scratch
custom-types.md	Make your own data type when the built-in ones do not fit
writing-plots.md	Write a quick preview-only plot of a result
examples/	Worked, runnable examples for every authoring surface: blocks, types, panels, plots, and workflows

How this guide works

These pages tell you what exists and how to use it, with worked examples. They deliberately do not restate every parameter and return type. For the exact contract of a class or method, the API reference (in the api-reference/ folder beside this guide, and published online) is generated directly from the code, so it can never be out of date. When a page names a symbol — say from scistudio.blocks.base import InputPort — that import path is the contract: import from there and your code keeps working across releases.

Two audiences, one boundary

If you are building a distributable package to share blocks with other people (the way the imaging, LC-MS, and spectroscopy packages are built), that is a separate guide aimed at developers — see Package Development (docs/package-development/) in the SciStudio repository. This guide is for using SciStudio in your own project.