abba-mcp 0.25.0__tar.gz

abba_mcp-0.25.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 UNIGE
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

abba_mcp-0.25.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: abba-mcp
+Version: 0.25.0
+Summary: MCP server for ABBA (Aligning Big Brains and Atlases): an AI assistant registers brain sections to atlases in a pinned Fiji
+Author-email: Nicolas Chiaruttini <nicolas.chiaruttini@unige.ch>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/unige-biochem/abba-mcp
+Project-URL: Issues, https://github.com/unige-biochem/abba-mcp/issues
+Project-URL: Documentation, https://abba-documentation.readthedocs.io
+Keywords: mcp,abba,fiji,imagej,brain atlas,registration,neuroscience
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mcp<2,>=1.9
+Requires-Dist: jgo[cli]>=3.1
+Requires-Dist: cjdk>=0.5
+Dynamic: license-file
+
+# abba-mcp: ABBA for AI assistants (experimental)
+
+Lets an AI assistant drive [ABBA](https://abba-documentation.readthedocs.io) (Aligning Big Brains and Atlases) to
+register brain sections to an atlas. The assistant runs ABBA's commands, looks at what they produced, and once the
+result is right saves the session (`.abba` state file) and a Groovy script that replays every step.
+
+You can follow along and take over at any time: by default, ABBA's window opens on your screen as usual.
+
+It is an [MCP](https://modelcontextprotocol.io) server, so it is not tied to one assistant: it works with any
+application (MCP client) that can start a local MCP server, and any model it offers that calls tools and reads
+images (the assistant looks at pictures of your slices).
+
+## Install
+
+You need [uv](https://docs.astral.sh/uv/getting-started/installation/) and an internet connection for the first
+run. Java, Fiji and ABBA are downloaded for you.
+
+### Claude
+
+- **Claude Desktop**: download `abba-mcp-<version>.mcpb` from the
+  [releases](https://github.com/unige-biochem/abba-mcp/releases) and double-click it.
+- **Claude Code**:
+  ```
+  claude mcp add abba -- uvx abba-mcp
+  ```
+
+### VS Code (GitHub Copilot)
+
+[![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_ABBA_MCP-0098FF?logo=visualstudiocode)](https://vscode.dev/redirect/mcp/install?name=abba&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22abba-mcp%22%5D%7D)
+
+Or, from a terminal: `code --add-mcp '{"name":"abba","command":"uvx","args":["abba-mcp"]}'`.
+
+### OpenAI
+
+- **Codex** (CLI, IDE extension), and the **ChatGPT desktop app**, which shares Codex's configuration:
+  ```
+  codex mcp add abba -- uvx abba-mcp
+  ```
+- **ChatGPT on the web** connects to remote MCP servers only: it cannot start this one.
+
+### Any other MCP client
+
+The server talks MCP over stdio (protocol versions 2024-11-05 to 2025-11-25): command `uvx`, arguments
+`abba-mcp`. Most applications (Cursor, Gemini CLI...) take this JSON in their MCP settings:
+
+```json
+{
+  "mcpServers": {
+    "abba": {
+      "command": "uvx",
+      "args": ["abba-mcp"]
+    }
+  }
+}
+```
+
+`uvx abba-mcp` runs the latest release; `uvx abba-mcp@0.25.0` a given one (the version is the ABBA it runs).
+
+The server gives the assistant its rules and points it to its documentation through the MCP *instructions*.
+Some applications do not pass them on: if the assistant seems not to know how to proceed, ask it to read
+`guides/abba.md` with the `abba_docs_read` tool first.
+
+## First run
+
+The first time the assistant uses Fiji, the server downloads Java, Fiji and ABBA, then starts them: allow several
+minutes; later starts are much faster. Meanwhile the assistant is told that Fiji is starting, and tries again. DeepSlice, Elastix and atlases are also downloaded the first time they are
+needed.
+
+## With or without a window
+
+- **Window** (default): ABBA opens its window on your screen. You see what the assistant does, can select slices
+  for it, and can take over.
+- **Headless**: no window, for servers and remote machines. The assistant shows you snapshots instead, and
+  manual registrations are not available. Set the environment variable `ABBA_MCP_HEADLESS=true` for the server:
+  `"env": {"ABBA_MCP_HEADLESS": "true"}` next to `"args"` in the JSON, `-e ABBA_MCP_HEADLESS=true` before `--`
+  for `claude mcp add`, `--env ABBA_MCP_HEADLESS=true` for `codex mcp add`. In Claude Desktop, turn on
+  *Run Fiji without a window* in the extension's settings.
+
+## Privacy
+
+What the assistant looks at (snapshots of your slices, the session state, file names) is sent to your AI
+provider, as for anything else you show it. Fiji itself is only reachable from your own computer (port 9090 on
+127.0.0.1).
+
+## Versions
+
+The version is the ABBA version it runs (`0.25.0`), with `.post1`, `.post2`... for a fix of this server alone.
+Every machine gets the same Fiji, ABBA and plugins, and the assistant's documentation is written for exactly that
+version. Your own Fiji installation is not used or modified.
+
+## Troubleshooting
+
+- **"The Fiji on port 9090 runs ..."**: another Fiji with an MCP server is already running (your own, or one
+  started by another version of this bundle). Close it and ask again.
+- **Fiji does not start**: its log is `fiji.log` in `~/.abba-mcp` (set `ABBA_MCP_HOME` to use another folder).
+- Questions about ABBA itself: the [ABBA documentation](https://abba-documentation.readthedocs.io/en/v0.25.0/) of this version and the
+  [image.sc forum](https://forum.image.sc/tag/abba).
+
+Developing or releasing this bundle: see [DEVELOPMENT.md](DEVELOPMENT.md).

abba_mcp-0.25.0/README.md

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+# abba-mcp: ABBA for AI assistants (experimental)
+
+Lets an AI assistant drive [ABBA](https://abba-documentation.readthedocs.io) (Aligning Big Brains and Atlases) to
+register brain sections to an atlas. The assistant runs ABBA's commands, looks at what they produced, and once the
+result is right saves the session (`.abba` state file) and a Groovy script that replays every step.
+
+You can follow along and take over at any time: by default, ABBA's window opens on your screen as usual.
+
+It is an [MCP](https://modelcontextprotocol.io) server, so it is not tied to one assistant: it works with any
+application (MCP client) that can start a local MCP server, and any model it offers that calls tools and reads
+images (the assistant looks at pictures of your slices).
+
+## Install
+
+You need [uv](https://docs.astral.sh/uv/getting-started/installation/) and an internet connection for the first
+run. Java, Fiji and ABBA are downloaded for you.
+
+### Claude
+
+- **Claude Desktop**: download `abba-mcp-<version>.mcpb` from the
+  [releases](https://github.com/unige-biochem/abba-mcp/releases) and double-click it.
+- **Claude Code**:
+  ```
+  claude mcp add abba -- uvx abba-mcp
+  ```
+
+### VS Code (GitHub Copilot)
+
+[![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_ABBA_MCP-0098FF?logo=visualstudiocode)](https://vscode.dev/redirect/mcp/install?name=abba&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22abba-mcp%22%5D%7D)
+
+Or, from a terminal: `code --add-mcp '{"name":"abba","command":"uvx","args":["abba-mcp"]}'`.
+
+### OpenAI
+
+- **Codex** (CLI, IDE extension), and the **ChatGPT desktop app**, which shares Codex's configuration:
+  ```
+  codex mcp add abba -- uvx abba-mcp
+  ```
+- **ChatGPT on the web** connects to remote MCP servers only: it cannot start this one.
+
+### Any other MCP client
+
+The server talks MCP over stdio (protocol versions 2024-11-05 to 2025-11-25): command `uvx`, arguments
+`abba-mcp`. Most applications (Cursor, Gemini CLI...) take this JSON in their MCP settings:
+
+```json
+{
+  "mcpServers": {
+    "abba": {
+      "command": "uvx",
+      "args": ["abba-mcp"]
+    }
+  }
+}
+```
+
+`uvx abba-mcp` runs the latest release; `uvx abba-mcp@0.25.0` a given one (the version is the ABBA it runs).
+
+The server gives the assistant its rules and points it to its documentation through the MCP *instructions*.
+Some applications do not pass them on: if the assistant seems not to know how to proceed, ask it to read
+`guides/abba.md` with the `abba_docs_read` tool first.
+
+## First run
+
+The first time the assistant uses Fiji, the server downloads Java, Fiji and ABBA, then starts them: allow several
+minutes; later starts are much faster. Meanwhile the assistant is told that Fiji is starting, and tries again. DeepSlice, Elastix and atlases are also downloaded the first time they are
+needed.
+
+## With or without a window
+
+- **Window** (default): ABBA opens its window on your screen. You see what the assistant does, can select slices
+  for it, and can take over.
+- **Headless**: no window, for servers and remote machines. The assistant shows you snapshots instead, and
+  manual registrations are not available. Set the environment variable `ABBA_MCP_HEADLESS=true` for the server:
+  `"env": {"ABBA_MCP_HEADLESS": "true"}` next to `"args"` in the JSON, `-e ABBA_MCP_HEADLESS=true` before `--`
+  for `claude mcp add`, `--env ABBA_MCP_HEADLESS=true` for `codex mcp add`. In Claude Desktop, turn on
+  *Run Fiji without a window* in the extension's settings.
+
+## Privacy
+
+What the assistant looks at (snapshots of your slices, the session state, file names) is sent to your AI
+provider, as for anything else you show it. Fiji itself is only reachable from your own computer (port 9090 on
+127.0.0.1).
+
+## Versions
+
+The version is the ABBA version it runs (`0.25.0`), with `.post1`, `.post2`... for a fix of this server alone.
+Every machine gets the same Fiji, ABBA and plugins, and the assistant's documentation is written for exactly that
+version. Your own Fiji installation is not used or modified.
+
+## Troubleshooting
+
+- **"The Fiji on port 9090 runs ..."**: another Fiji with an MCP server is already running (your own, or one
+  started by another version of this bundle). Close it and ask again.
+- **Fiji does not start**: its log is `fiji.log` in `~/.abba-mcp` (set `ABBA_MCP_HOME` to use another folder).
+- Questions about ABBA itself: the [ABBA documentation](https://abba-documentation.readthedocs.io/en/v0.25.0/) of this version and the
+  [image.sc forum](https://forum.image.sc/tag/abba).
+
+Developing or releasing this bundle: see [DEVELOPMENT.md](DEVELOPMENT.md).

abba_mcp-0.25.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "abba-mcp"
+version = "0.25.0"
+description = "MCP server for ABBA (Aligning Big Brains and Atlases): an AI assistant registers brain sections to atlases in a pinned Fiji"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+authors = [{ name = "Nicolas Chiaruttini", email = "nicolas.chiaruttini@unige.ch" }]
+keywords = ["mcp", "abba", "fiji", "imagej", "brain atlas", "registration", "neuroscience"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Image Processing",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = [
+    "mcp>=1.9,<2",
+    "jgo[cli]>=3.1",
+    "cjdk>=0.5",  # the pinned JDK (env/jgo.toml [java]); also a dependency of jgo
+]
+
+[project.urls]
+Homepage = "https://github.com/unige-biochem/abba-mcp"
+Issues = "https://github.com/unige-biochem/abba-mcp/issues"
+Documentation = "https://abba-documentation.readthedocs.io"
+
+[project.scripts]
+abba-mcp = "abba_mcp:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"abba_mcp" = ["fiji_tools.json", "env/*", "data/**/*"]

abba_mcp-0.25.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+