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MedICS user guide

What MedICS can do, and how to use it. This guide covers the workspace, the built-in toolboxes, Python, settings, the AI assistant and the official extensions. New to MedICS? Start with Get started to install and launch it.

The MedICS main window
The MedICS window. Tools open as tabs, with the File Explorer, workspace variables and the bottom panel (Logging · Terminal · Jupyter · Results) around them.

What MedICS is

MedICS (Medical Image Computing Suite) is a desktop application for loading, inspecting and analyzing medical images. Image viewing, Python scripting, data import and third-party tools all live in one window instead of being spread across separate programs.

Key features

AreaWhat you get
Image I/OOpen DICOM (including JPEG 2000 and OCT series), TIFF stacks, NIfTI, HDF5, MATLAB .mat, PNG/JPEG, video and more.
PreviewInspect images, volumes, tables, Markdown and code — with slice navigation and window/level, without changing the file.
ImportLoad image sequences, single files and whole DICOM folders, with drag-and-drop and background progress.
PythonAn interactive console and the PyEditor IDE share one live workspace.
WorkspaceKeep every result in a named workspace and save it to a .med file.
ToolboxesFilePreview, ImportData, PyEditor and JupyterLab open as tabs beside your work.
ExtensionsAdd new tools and panels from installable packages — no rebuild of MedICS required.
AI assistantAsk questions or hand off multi-step tasks; each action that changes data needs your approval.

Supported formats

TypeFormats
ImagesPNG, JPEG, BMP, GIF, WebP, ICO, PPM/PGM/PBM, SVG, single-frame TIFF
VolumesNIfTI, MetaImage, DICOM series, stacked TIFF, MedICS image bundles
Scientific containersHDF5, MedICS .med, MATLAB .mat, NumPy .npy/.npz
TablesCSV, TSV, Excel, Parquet
DocumentsMarkdown, plain text and source code
VideoMP4, AVI, MKV, MOV, WebM, WMV, M4V, MPG/MPEG, OGV, 3GP

The panels

Show or hide panels from the View menu. Interface & components →

File Explorer
File Explorer
Variables
Variables
Logging
Logging
Jupyter console
Jupyter console
Terminal
Terminal
Agent chat
Agent chat

The toolboxes

Built-in tools that open as tabs. Toolboxes →

<strong>ImportData</strong> — load images and volumes.
ImportData — load images and volumes.
<strong>FilePreview</strong> — preview images and volumes.
FilePreview — preview images and volumes.
<strong>PyEditor</strong> — the Python editor.
PyEditor — the Python editor.
<strong>JupyterLab</strong> — notebooks in a tab.
JupyterLab — notebooks in a tab.

Read the guide

Basics

Basics

Interface & components

The MedICS window and its panels: File Explorer, Variables, Logging, Terminal, Jupyter console, Results and Agent chat.

Basics

Settings & preferences

Appearance, logging, window behaviour, extensions, the AI provider and the MedICS token.

Features

Features

Toolboxes

The built-in tools — FilePreview, ImportData, PyEditor and JupyterLab — and how to use them.

Features

AI assistant

Ask questions and let the assistant perform tasks in MedICS, with your approval.

Official Extensions

Official Extensions

Retinal Layer Segmentation

AI segmentation of retinal layers in OCT/OCTA volumes — detect the layer boundaries, review and edit them, interpolate across B-scans, and export the results.

Official Extensions

Volume Labeler

Paint labels on the B-frames or en-face projection of a 3-D volume, constrain work to a slab, measure each label, inspect it in 3-D, and export label maps.

Looking for more? Extensions shows how to add tools to MedICS, and the MedICS Wiki has community tips and examples.