ImageJAI is an ImageJ/Fiji plugin for describing image analysis in plain language. It offers an assistant inside Fiji and a standalone terminal console. The agent can inspect open images, run macros, read measurements, interact with plugin dialogs and check the result while the user supervises.
Users can choose a cloud model, a supported agent subscription or a local model through Ollama. Model access is configured separately from the plugin.
Installation
- Start Fiji and choose Help › Update….
- Click Manage update sites.
- Enable ImageJAI if listed. Otherwise add an unlisted site with the name
ImageJ-AIand URLhttps://sites.imagej.net/ImageJ-AI/. - Apply changes and restart Fiji.
- Open Plugins › AI Assistant.
Fiji must run Java 11 or newer. The embedded assistant runs from the plugin JAR. The optional console requires internet access for its first setup.
Standalone console setup
In the assistant, open Settings > Models & Agents, find ImageJAI Console and click Install. The plugin creates a private Python environment and installs the console’s packages. If suitable Python is unavailable, it downloads a private Python runtime; a manual Python installation is not required. Setup does not require administrator access.
Launch the console from the same settings row, or run imagejai in a terminal.
Choose a model and sign in to its supported provider or connect to a local
model server. Provider subscriptions and usage charges are separate from
ImageJAI.
Working with Fiji
For example, ask the assistant to open the sample Blobs image, blur it, segment objects, measure fluorescence or export the results. ImageJAI uses Fiji’s available commands and can inspect unfamiliar plugin dialogs before running them. It operates on open Fiji images, results tables and regions of interest; supported file formats depend on the installed Fiji plugins.
The console detects or uses a saved Fiji installation. It can launch Fiji
and start ImageJAI’s local TCP server automatically. Use /fiji to select
another installation and /settings to configure startup.
| Console control | Purpose |
|---|---|
/model |
Choose a model and its available reasoning effort levels |
/settings |
Configure the agent, Fiji, privacy, display and budget |
| Session Macros | Browse and reuse the current session’s macros |
/help |
Show commands and keyboard controls |
Replies and activity are streamed into the conversation. Tool results have short summaries with expandable details, and side panels can collapse to give the chat more space. Saved sessions can be resumed later.
Outputs and records
Analyses can create Fiji images, measurements and results tables. Exported
analysis files are written under AI_Exports/ next to the source image.
The console records session macros and conversation history, allowing the
user to review or reuse the work.
Privacy controls
New folders use Standard posture, which permits original filenames and metadata in agent responses. Users can select Pseudonymised to filter supported identifiers or On-premises to restrict supported launch routes to local models. Saved folder choices are retained.
These controls cover ImageJAI’s supported routes and responses. They do not anonymise source images or govern tools outside ImageJAI. See the privacy guide for the scope and limits.
Scripting and external agents
ImageJAI exposes authenticated JSON commands through a local TCP server, normally on port 7746. The public command documentation covers macro and script execution, image inspection, results, dialogs and event subscriptions. See the command reference and console guide.
