Metadata-Version: 2.4
Name: mesofield
Version: 0.3.2b0
Summary: Mesofield is an open-source image acquisition Python software package build for the Sipe Laboratory at Pennsylvania State University.
Author: Jacob Gronemeyer
License: MIT License
        
        Copyright (c) 2024 Gronemeyer
        
        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.
        
Project-URL: Homepage, https://github.com/Gronemeyer/mesofield/
Project-URL: Repository, https://github.com/Gronemeyer/mesofield/
Project-URL: Issues, https://github.com/Gronemeyer/mesofield/issues
Project-URL: Documentation, https://gronemeyer.github.io/mesofield/
Keywords: imaging,microscopy,acquisition,neuroscience
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: annotated-types
Requires-Dist: click
Requires-Dist: ipykernel
Requires-Dist: ipython
Requires-Dist: jupyter_client
Requires-Dist: jupyter_core
Requires-Dist: loguru
Requires-Dist: markdown-it-py
Requires-Dist: matplotlib
Requires-Dist: mesokit-schema
Requires-Dist: nidaqmx
Requires-Dist: numpy
Requires-Dist: packaging
Requires-Dist: pandas
Requires-Dist: parso
Requires-Dist: pillow
Requires-Dist: platformdirs
Requires-Dist: psygnal
Requires-Dist: pyaml
Requires-Dist: opencv-python
Requires-Dist: pymmcore
Requires-Dist: pymmcore-plus
Requires-Dist: pymmcore-widgets
Requires-Dist: PyQt6
Requires-Dist: PyQt6-Qt6
Requires-Dist: PyQt6_sip
Requires-Dist: pyqtgraph
Requires-Dist: pyserial
Requires-Dist: python-dateutil
Requires-Dist: pytz
Requires-Dist: pywin32; sys_platform == "win32"
Requires-Dist: pyzmq
Requires-Dist: qtconsole
Requires-Dist: rich
Requires-Dist: setuptools
Requires-Dist: tifffile
Requires-Dist: typer
Requires-Dist: typer-slim
Requires-Dist: typing_extensions
Requires-Dist: useq-schema
Requires-Dist: wheel
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: coverage; extra == "test"
Requires-Dist: flake8; extra == "test"
Requires-Dist: black; extra == "test"
Requires-Dist: isort; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Requires-Dist: mypy; extra == "test"
Requires-Dist: gitchangelog; extra == "test"
Provides-Extra: docs
Requires-Dist: sphinx>=7; extra == "docs"
Requires-Dist: pydata-sphinx-theme; extra == "docs"
Requires-Dist: myst-parser; extra == "docs"
Requires-Dist: sphinx-copybutton; extra == "docs"
Requires-Dist: sphinx-design; extra == "docs"
Dynamic: license-file

```
 __    __     ______     ______     ______     ______   __     ______     __         _____
/\ "-./  \   /\  ___\   /\  ___\   /\  __ \   /\  ___\ /\ \   /\  ___\   /\ \       /\  __-.
\ \ \-./\ \  \ \  __\   \ \___  \  \ \ \/\ \  \ \  __\ \ \ \  \ \  __\   \ \ \____  \ \ \/\ \
 \ \_\ \ \_\  \ \_____\  \/\_____\  \ \_____\  \ \_\    \ \_\  \ \_____\  \ \_____\  \ \____-
  \/_/  \/_/   \/_____/   \/_____/   \/_____/   \/_/     \/_/   \/_____/   \/_____/   \/____/
```

Mesofield is a PyQt6-based framework for running real-time, multi-camera
neuroscience experiments. It coordinates hardware via serial connections
and MicroManager (through [pymmcore-plus](https://pymmcore-plus.github.io/pymmcore-plus/)
custom `MDAEngine`s and multi-`CMMCorePlus` instancing) and manages
experiment configuration, acquisition orchestration, and data logging.
The project is aimed at laboratory use and is not a full production
package; some specialised knowledge of device hardware and
MicroManager device configuration is necessary to get started.

<img width="2454" height="1592" alt="Mesofield acquisition window" src="https://github.com/user-attachments/assets/151196ab-2d74-4644-85b7-c4facf3b779a" />

---

## Documentation

Documentation lives at **[gronemeyer.github.io/mesofield](https://gronemeyer.github.io/mesofield/)**
and is split by audience:

- **[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html)** —
  the fastest path from a fresh conda env to a working acquisition on
  your hardware.
- **[User Guide](https://gronemeyer.github.io/mesofield/user_guide.html)** —
  for experimenters running acquisitions: launching the GUI, writing
  `experiment.json`, interpreting the on-disk output.
- **[Developer Guide](https://gronemeyer.github.io/mesofield/developer_guide.html)** —
  for developers extending mesofield: custom devices, `Procedure`
  subclasses, frame processors, threading models.
- **[API Reference](https://gronemeyer.github.io/mesofield/api/index.html)** —
  auto-generated from docstrings.

---

## Quick start

```bash
conda create -n mesofield python=3.12 -y
conda activate mesofield
pip install -e .
```

Launch an acquisition:

```bash
mesofield launch path/to/experiment.json
```

Scaffold a new experiment:

```bash
mesofield new my-experiment
```

For end-to-end setup, follow the
[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html).

---

## System requirements

Tested on Windows 10/11. For multi-camera acquisition with large files
we recommend ≥ 32 GB RAM, a 12th-gen Intel i7 or equivalent, and fast
local NVMe storage for the experiment directory.

---

## License

MIT — see `LICENSE`.
