PyPI - lbm_suite2p_python - Versions diffs - 2.5.1__tar.gz → 2.5.2__tar.gz - Mend

lbm_suite2p_python 2.5.1tar.gz → 2.5.2tar.gz

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{lbm_suite2p_python-2.5.1 → lbm_suite2p_python-2.5.2}/LICENSE.md RENAMED Viewed

@@ -1,17 +1,17 @@
-This software license is the 3-clause BSD license plus a fourth clause that prohibits redistribution for commercial purposes without further permission.
-BSD 3-Clause License
-Copyright (c) 2024, Miller Brain Observatory.
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-Redistributions for commercial purposes are not permitted without the written permission of all code authors. For purposes of this license, commercial purposes is the incorporation of LBM-Suite2p-Python into anything for which you will charge fees or other compensation. Contact mbo@rockefeller.edu for more information.
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+This software license is the 3-clause BSD license plus a fourth clause that prohibits redistribution for commercial purposes without further permission.
+BSD 3-Clause License
+Copyright (c) 2024, Miller Brain Observatory.
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+Redistributions for commercial purposes are not permitted without the written permission of all code authors. For purposes of this license, commercial purposes is the incorporation of LBM-Suite2p-Python into anything for which you will charge fees or other compensation. Contact mbo@rockefeller.edu for more information.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

{lbm_suite2p_python-2.5.1/lbm_suite2p_python.egg-info → lbm_suite2p_python-2.5.2}/PKG-INFO RENAMED Viewed

@@ -1,243 +1,243 @@
-Metadata-Version: 2.4
-Name: lbm_suite2p_python
-Version: 2.5.1
-Summary: Light Beads Microscopy Pipeline using Suite2p
-License-Expression: BSD-3-Clause
-Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
-Keywords: Pipeline,Numpy,Microscopy,ScanImage,Suite2p,tiff
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Science/Research
-Classifier: Programming Language :: Python :: 3 :: Only
-Requires-Python: <3.12.10,>=3.12.7
-Description-Content-Type: text/markdown
-License-File: LICENSE.md
-Requires-Dist: mbo_utilities>=2.4.3
-Provides-Extra: suite2p
-Requires-Dist: suite2p_mbo>=2.0.1; extra == "suite2p"
-Provides-Extra: rastermap
-Requires-Dist: rastermap; extra == "rastermap"
-Provides-Extra: cellpose
-Requires-Dist: cellpose>=4.0.6; extra == "cellpose"
-Provides-Extra: torch
-Requires-Dist: torch>=2.7.0; extra == "torch"
-Requires-Dist: torchvision>=0.22.0; extra == "torch"
-Provides-Extra: all
-Requires-Dist: lbm_suite2p_python[cellpose,rastermap,suite2p,torch]; extra == "all"
-Dynamic: license-file
-<p align="center">
-<img src="docs/_static/logo_suit2p.png" height="180" alt="LBM-Suite2p-Python logo">
-</p>
-<p align="center">
-<a href="https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/actions/workflows/test_python.yml"><img src="https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/actions/workflows/test_python.yml/badge.svg" alt="Tests"></a>
-<a href="https://badge.fury.io/py/lbm-suite2p-python"><img src="https://badge.fury.io/py/lbm-suite2p-python.svg" alt="PyPI version"></a>
-<a href="https://millerbrainobservatory.github.io/LBM-Suite2p-Python/"><img src="https://img.shields.io/badge/docs-online-green" alt="Documentation"></a>
-<a href="https://doi.org/10.1038/s41592-021-01239-8"><img src="https://zenodo.org/badge/DOI/10.1007/978-3-319-76207-4_15.svg" alt="DOI"></a>
-</p>
-<p align="center">
-<a href="#installation"><b>Installation</b></a> ·
-<a href="https://millerbrainobservatory.github.io/LBM-Suite2p-Python/"><b>Documentation</b></a> ·
-<a href="https://millerbrainobservatory.github.io/LBM-Suite2p-Python/user_guide.html"><b>User Guide</b></a> ·
-<a href="https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/issues"><b>Issues</b></a>
-</p>
-A volumetric 2-photon calcium imaging processing pipeline for [Light Beads Microscopy](https://github.com/MillerBrainObservatory) (LBM) datasets, built on Suite2p.
-- **Process volumetric calcium imaging data** - motion correction, cell detection, and signal extraction across z-planes
-- **Automated quality diagnostics** - ROI quality metrics, ΔF/F traces, and correlation maps
-- **Scalable architecture** - process single planes or entire volumes with consistent parameters
-<p align="center">
-<img src="docs/_images/volume/all_planes_masks.png" height="180" alt="All Planes Masks" /><img src="docs/_images/outputs/08_traces_dff.png" height="180" alt="ΔF/F Traces" /><img src="docs/_images/volume/roi_map_3d.png" height="180" alt="3D ROI Map" />
-<br/>
-<em>Planar Suite2p outputs combined into a 3D representation of neural activity</em>
-</p>
-> **Note:**
-> `lbm_suite2p_python` is in **late-beta** stage of active development. File an [issue](https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/issues) for bugs or feature requests.
-## Installation
-`lbm_suite2p_python` is available on [PyPI](https://pypi.org/project/lbm-suite2p-python/):
-> We recommend using a virtual environment. For help setting up a virtual environment, see [the MBO guide on virtual environments](https://millerbrainobservatory.github.io/guides/venvs.html).
-```bash
-# create a new project folder
-mkdir my_project && cd my_project
-# create environment and install (uv recommended)
-uv venv --python 3.12.9
-uv pip install lbm_suite2p_python
-# or with pip
-pip install lbm_suite2p_python
-```
-### Optional Dependencies
-```bash
-# With rastermap for activity clustering visualization
-uv pip install "lbm_suite2p_python[rastermap]"
-# With cellpose for anatomical cell detection (includes PyTorch)
-uv pip install "lbm_suite2p_python[cellpose]"
-# All optional dependencies
-uv pip install "lbm_suite2p_python[all]"
-```
-### Development Installation
-```bash
-git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
-cd LBM-Suite2p-Python
-uv pip install -e ".[dev]"
-```
-## Quick Start
-```python
-import lbm_suite2p_python as lsp
-results = lsp.pipeline(
-    input_data="D:/data/raw",   # path to file, directory, or list of files
-    save_path=None,             # default: save next to input
-    ops=None,                   # default: use MBO-optimized parameters
-    planes=None,                # default: process all planes (1-indexed)
-    roi_mode=None,              # default: stitch multi-ROI data
-    keep_reg=True,              # default: keep data.bin (registered binary)
-    keep_raw=False,             # default: delete data_raw.bin after processing
-    force_reg=False,            # default: skip if already registered
-    force_detect=False,         # default: skip if stat.npy exists
-    dff_window_size=None,       # default: auto-calculate from tau and framerate
-    dff_percentile=20,          # default: 20th percentile for baseline
-    dff_smooth_window=None,     # default: auto-calculate from tau and framerate
-)
-```
-> [User Guide](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/user_guide.html) for full API reference and examples
-## Output Gallery
-### Planar Results
-Each z-plane produces diagnostic images automatically saved during processing.
-<p align="center">
-<table>
-<tr>
-<td align="center">
-<img src="docs/_images/outputs/01_correlation_segmentation.png" alt="Correlation Segmentation" width="280"/>
-<br/><em>correlation image with ROI overlay</em>
-</td>
-<td align="center">
-<img src="docs/_images/outputs/03_mean_segmentation.png" alt="Mean Segmentation" width="280"/>
-<br/><em>mean image with ROI overlay</em>
-</td>
-</tr>
-<tr>
-<td align="center">
-<img src="docs/_images/outputs/05_quality_diagnostics.png" alt="Quality Diagnostics" width="280"/>
-<br/><em>ROI quality metrics</em>
-</td>
-<td align="center">
-<img src="docs/_images/outputs/08_traces_dff.png" alt="ΔF/F Traces" width="280"/>
-<br/><em>ΔF/F traces sorted by quality</em>
-</td>
-</tr>
-</table>
-</p>
-### Volumetric Results
-Volume-level visualizations combine data across all z-planes.
-<p align="center">
-<table>
-<tr>
-<td align="center">
-<img src="docs/_images/volume/orthoslices.png" alt="Orthoslices" width="300"/>
-<br/><em>XZ/YZ orthogonal projections</em>
-</td>
-<td align="center">
-<img src="docs/_images/volume/rastermap.png" alt="Rastermap" width="400"/>
-<br/><em>activity sorted by similarity (rastermap)</em>
-</td>
-</tr>
-</table>
-</p>
-## GUI
-A graphical interface is available via [mbo_utilities](https://millerbrainobservatory.github.io/mbo_utilities/index.html#gui):
-```bash
-pip install mbo_utilities
-mbo                    # launch GUI
-mbo /path/to/data      # open file directly
-```
-> **Note:** GUI functionality may lag behind the latest pipeline features.
-## Troubleshooting
-<details>
-<summary><b>Git LFS Download Errors</b></summary>
-If you see `smudge filter lfs failed` when installing from GitHub:
-```bash
-GIT_LFS_SKIP_SMUDGE=1 uv pip install git+https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
-```
-Or set it permanently:
-```powershell
-# Windows
-[System.Environment]::SetEnvironmentVariable('GIT_LFS_SKIP_SMUDGE', '1', 'User')
-```
-```bash
-# Linux/macOS
-echo 'export GIT_LFS_SKIP_SMUDGE=1' >> ~/.bashrc
-source ~/.bashrc
-```
-</details>
-<details>
-<summary><b>GUI Dependencies</b></summary>
-**Linux / macOS:**
-```bash
-sudo apt install libxcursor-dev libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev
-```
-**Windows:**
-Install [Microsoft Visual C++ Redistributable](https://learn.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist)
-</details>
-## Built With
-- **[Suite2p](https://github.com/MouseLand/suite2p)** - Core registration and segmentation
-- **[Cellpose](https://github.com/MouseLand/cellpose)** - Anatomical segmentation (optional)
-- **[Rastermap](https://github.com/MouseLand/rastermap)** - Activity clustering (optional)
-- **[mbo_utilities](https://github.com/MillerBrainObservatory/mbo_utilities)** - ScanImage I/O and metadata
-## Issues & Support
-- **Bug reports:** [GitHub Issues](https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/issues)
-- **Questions:** See [documentation](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/) or [Suite2p docs](https://suite2p.readthedocs.io/)
-## Contributing
-Contributions are welcome! This project uses:
-- **Ruff** for linting and formatting (line length: 88, numpy docstring style)
-- **pytest** for testing
-- **Sphinx** for documentation
+Metadata-Version: 2.4
+Name: lbm_suite2p_python
+Version: 2.5.2
+Summary: Light Beads Microscopy Pipeline using Suite2p
+License-Expression: BSD-3-Clause
+Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
+Keywords: Pipeline,Numpy,Microscopy,ScanImage,Suite2p,tiff
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: <3.12.10,>=3.12.7
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: mbo_utilities>=2.5.0
+Provides-Extra: suite2p
+Requires-Dist: suite2p_mbo>=2.0.1; extra == "suite2p"
+Provides-Extra: rastermap
+Requires-Dist: rastermap; extra == "rastermap"
+Provides-Extra: cellpose
+Requires-Dist: cellpose>=4.0.6; extra == "cellpose"
+Provides-Extra: torch
+Requires-Dist: torch>=2.7.0; extra == "torch"
+Requires-Dist: torchvision>=0.22.0; extra == "torch"
+Provides-Extra: all
+Requires-Dist: lbm_suite2p_python[cellpose,rastermap,suite2p,torch]; extra == "all"
+Dynamic: license-file
+<p align="center">
+<img src="docs/_static/logo_suit2p.png" height="180" alt="LBM-Suite2p-Python logo">
+</p>
+<p align="center">
+<a href="https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/actions/workflows/test_python.yml"><img src="https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/actions/workflows/test_python.yml/badge.svg" alt="Tests"></a>
+<a href="https://badge.fury.io/py/lbm-suite2p-python"><img src="https://badge.fury.io/py/lbm-suite2p-python.svg" alt="PyPI version"></a>
+<a href="https://millerbrainobservatory.github.io/LBM-Suite2p-Python/"><img src="https://img.shields.io/badge/docs-online-green" alt="Documentation"></a>
+<a href="https://doi.org/10.1038/s41592-021-01239-8"><img src="https://zenodo.org/badge/DOI/10.1007/978-3-319-76207-4_15.svg" alt="DOI"></a>
+</p>
+<p align="center">
+<a href="#installation"><b>Installation</b></a> ·
+<a href="https://millerbrainobservatory.github.io/LBM-Suite2p-Python/"><b>Documentation</b></a> ·
+<a href="https://millerbrainobservatory.github.io/LBM-Suite2p-Python/user_guide.html"><b>User Guide</b></a> ·
+<a href="https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/issues"><b>Issues</b></a>
+</p>
+A volumetric 2-photon calcium imaging processing pipeline for [Light Beads Microscopy](https://github.com/MillerBrainObservatory) (LBM) datasets, built on Suite2p.
+- **Process volumetric calcium imaging data** - motion correction, cell detection, and signal extraction across z-planes
+- **Automated quality diagnostics** - ROI quality metrics, ΔF/F traces, and correlation maps
+- **Scalable architecture** - process single planes or entire volumes with consistent parameters
+<p align="center">
+<img src="docs/_images/volume/all_planes_masks.png" height="180" alt="All Planes Masks" /><img src="docs/_images/outputs/08_traces_dff.png" height="180" alt="ΔF/F Traces" /><img src="docs/_images/volume/roi_map_3d.png" height="180" alt="3D ROI Map" />
+<br/>
+<em>Planar Suite2p outputs combined into a 3D representation of neural activity</em>
+</p>
+> **Note:**
+> `lbm_suite2p_python` is in **late-beta** stage of active development. File an [issue](https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/issues) for bugs or feature requests.
+## Installation
+`lbm_suite2p_python` is available on [PyPI](https://pypi.org/project/lbm-suite2p-python/):
+> We recommend using a virtual environment. For help setting up a virtual environment, see [the MBO guide on virtual environments](https://millerbrainobservatory.github.io/guides/venvs.html).
+```bash
+# create a new project folder
+mkdir my_project && cd my_project
+# create environment and install (uv recommended)
+uv venv --python 3.12.9
+uv pip install lbm_suite2p_python
+# or with pip
+pip install lbm_suite2p_python
+```
+### Optional Dependencies
+```bash
+# With rastermap for activity clustering visualization
+uv pip install "lbm_suite2p_python[rastermap]"
+# With cellpose for anatomical cell detection (includes PyTorch)
+uv pip install "lbm_suite2p_python[cellpose]"
+# All optional dependencies
+uv pip install "lbm_suite2p_python[all]"
+```
+### Development Installation
+```bash
+git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
+cd LBM-Suite2p-Python
+uv pip install -e ".[dev]"
+```
+## Quick Start
+```python
+import lbm_suite2p_python as lsp
+results = lsp.pipeline(
+    input_data="D:/data/raw",   # path to file, directory, or list of files
+    save_path=None,             # default: save next to input
+    ops=None,                   # default: use MBO-optimized parameters
+    planes=None,                # default: process all planes (1-indexed)
+    roi_mode=None,              # default: stitch multi-ROI data
+    keep_reg=True,              # default: keep data.bin (registered binary)
+    keep_raw=False,             # default: delete data_raw.bin after processing
+    force_reg=False,            # default: skip if already registered
+    force_detect=False,         # default: skip if stat.npy exists
+    dff_window_size=None,       # default: auto-calculate from tau and framerate
+    dff_percentile=20,          # default: 20th percentile for baseline
+    dff_smooth_window=None,     # default: auto-calculate from tau and framerate
+)
+```
+> [User Guide](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/user_guide.html) for full API reference and examples
+## Output Gallery
+### Planar Results
+Each z-plane produces diagnostic images automatically saved during processing.
+<p align="center">
+<table>
+<tr>
+<td align="center">
+<img src="docs/_images/outputs/01_correlation_segmentation.png" alt="Correlation Segmentation" width="280"/>
+<br/><em>correlation image with ROI overlay</em>
+</td>
+<td align="center">
+<img src="docs/_images/outputs/03_mean_segmentation.png" alt="Mean Segmentation" width="280"/>
+<br/><em>mean image with ROI overlay</em>
+</td>
+</tr>
+<tr>
+<td align="center">
+<img src="docs/_images/outputs/05_quality_diagnostics.png" alt="Quality Diagnostics" width="280"/>
+<br/><em>ROI quality metrics</em>
+</td>
+<td align="center">
+<img src="docs/_images/outputs/08_traces_dff.png" alt="ΔF/F Traces" width="280"/>
+<br/><em>ΔF/F traces sorted by quality</em>
+</td>
+</tr>
+</table>
+</p>
+### Volumetric Results
+Volume-level visualizations combine data across all z-planes.
+<p align="center">
+<table>
+<tr>
+<td align="center">
+<img src="docs/_images/volume/orthoslices.png" alt="Orthoslices" width="300"/>
+<br/><em>XZ/YZ orthogonal projections</em>
+</td>
+<td align="center">
+<img src="docs/_images/volume/rastermap.png" alt="Rastermap" width="400"/>
+<br/><em>activity sorted by similarity (rastermap)</em>
+</td>
+</tr>
+</table>
+</p>
+## GUI
+A graphical interface is available via [mbo_utilities](https://millerbrainobservatory.github.io/mbo_utilities/index.html#gui):
+```bash
+pip install mbo_utilities
+mbo                    # launch GUI
+mbo /path/to/data      # open file directly
+```
+> **Note:** GUI functionality may lag behind the latest pipeline features.
+## Troubleshooting
+<details>
+<summary><b>Git LFS Download Errors</b></summary>
+If you see `smudge filter lfs failed` when installing from GitHub:
+```bash
+GIT_LFS_SKIP_SMUDGE=1 uv pip install git+https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
+```
+Or set it permanently:
+```powershell
+# Windows
+[System.Environment]::SetEnvironmentVariable('GIT_LFS_SKIP_SMUDGE', '1', 'User')
+```
+```bash
+# Linux/macOS
+echo 'export GIT_LFS_SKIP_SMUDGE=1' >> ~/.bashrc
+source ~/.bashrc
+```
+</details>
+<details>
+<summary><b>GUI Dependencies</b></summary>
+**Linux / macOS:**
+```bash
+sudo apt install libxcursor-dev libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev
+```
+**Windows:**
+Install [Microsoft Visual C++ Redistributable](https://learn.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist)
+</details>
+## Built With
+- **[Suite2p](https://github.com/MouseLand/suite2p)** - Core registration and segmentation
+- **[Cellpose](https://github.com/MouseLand/cellpose)** - Anatomical segmentation (optional)
+- **[Rastermap](https://github.com/MouseLand/rastermap)** - Activity clustering (optional)
+- **[mbo_utilities](https://github.com/MillerBrainObservatory/mbo_utilities)** - ScanImage I/O and metadata
+## Issues & Support
+- **Bug reports:** [GitHub Issues](https://github.com/MillerBrainObservatory/LBM-Suite2p-Python/issues)
+- **Questions:** See [documentation](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/) or [Suite2p docs](https://suite2p.readthedocs.io/)
+## Contributing
+Contributions are welcome! This project uses:
+- **Ruff** for linting and formatting (line length: 88, numpy docstring style)
+- **pytest** for testing
+- **Sphinx** for documentation

lbm_suite2p_python 2.5.1__tar.gz → 2.5.2__tar.gz

lbm_suite2p_python 2.5.1tar.gz → 2.5.2tar.gz