Add ImageJAI plugin page

_pages/plugins/imagejai.md

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+---
+title: ImageJAI
+description: Conversational image analysis in Fiji with an embedded assistant, standalone console, cloud or local model selection, direct Fiji tools and reusable session macros.
+categories: [Analysis, Automation]
+source-url: https://github.com/Jay2owe/ImageJAI
+update-site: ImageJ-AI
+release-version: 0.5.0
+release-date: 2026-09-29
+dev-status: Active
+support-status: Active
+team-maintainers: '@Jay2owe'
+license-url: https://github.com/Jay2owe/ImageJAI/blob/main/LICENSE
+license-label: BSD-3-Clause
+---
+
+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
+
+1. Start Fiji and choose {% include bc path="Help|Update..." %}.
+2. Click **Manage update sites**.
+3. Enable **ImageJAI** if listed. Otherwise add an unlisted site with the name
+   `ImageJ-AI` and URL `https://sites.imagej.net/ImageJ-AI/`.
+4. Apply changes and restart Fiji.
+5. Open {% include bc path="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](https://github.com/Jay2owe/ImageJAI/blob/main/docs/data-governance/README.md)
+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](https://github.com/Jay2owe/ImageJAI/blob/main/docs/COMMAND_API.md)
+and [console guide](https://github.com/Jay2owe/ImageJAI/blob/main/docs/console/README.md).