PyPI - optimouse - Versions diffs - 0.1.0__tar.gz → 0.1.2__tar.gz - Mend

optimouse 0.1.0tar.gz → 0.1.2tar.gz

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{optimouse-0.1.0 → optimouse-0.1.2}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: optimouse
-Version: 0.1.0
+Version: 0.1.2
 Summary: 2-photon calcium imaging data processing pipeline with CaImAn / Suite2P
 Author-email: Vincent Prevosto <prevosto@mit.edu>, Manuel Levy <levym@mit.edu>
 License-Expression: MIT
@@ -20,7 +20,6 @@ Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: caiman<=1.13.0,>=1.12.2
 Requires-Dist: mesmerize-core>=0.5.0
 Requires-Dist: numpy>=1.26.4
 Requires-Dist: scipy>=1.15.3
@@ -37,38 +36,69 @@ Requires-Dist: ruff>=0.0.200; extra == "dev"
 Provides-Extra: viz
 Requires-Dist: fastplotlib>=0.1.0a16; extra == "viz"
 Requires-Dist: plotly>=6.5.2; extra == "viz"
+Provides-Extra: all
+Requires-Dist: pytest>=7.0.0; extra == "all"
+Requires-Dist: pytest-cov>=3.0.0; extra == "all"
+Requires-Dist: black>=22.0.0; extra == "all"
+Requires-Dist: ruff>=0.0.200; extra == "all"
+Requires-Dist: fastplotlib>=0.1.0a16; extra == "all"
+Requires-Dist: plotly>=6.5.2; extra == "all"
 Dynamic: license-file
 # 2P-proc (optimouse)
 [![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)](https://www.python.org/)
 [![CaImAn Version](https://img.shields.io/badge/CaImAn-1.12.2+-green)](https://github.com/flatironinstitute/CaImAn)
+[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
+[![DOI](https://zenodo.org/badge/1141473002.svg)](https://doi.org/10.5281/zenodo.18371949)
+<!-- [![Build Status](https://img.shields.io/github/actions/workflow/status/vncntprvst/2P-proc/ci.yml)](https://github.com/vncntprvst/2P-proc/actions) -->
 ![License](https://img.shields.io/badge/license-MIT-red)
-**2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/) and [Mesmerize](https://github.com/nel-lab/mesmerize-core/).
+**2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/), [Mesmerize](https://github.com/nel-lab/mesmerize-core/) and [Suite2p](https://github.com/MouseLand/suite2p).
 This package provides:
-- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction
-- **ROI extraction**: CNMF-based and Suite2p-based cell detection and segmentation
+- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid/non-rigid)
+- **ROI extraction**: CNMF-based or Suite2p-based cell detection and segmentation
 - **Spike deconvolution**: Temporal activity inference from calcium signals
-- **Parameter optimization**: Notebooks for systematic parameter exploration
+- **Parameter optimization**: Notebooks for systematic parameter exploration (CaImAn NoRMCorre and CNMF)
 - **Multi-session registration**: Cross-session ROI alignment using CaImAn's registration algorithm
+## No-installation Quick Start
+Try the pipeline without installation, using containers:
+* Create your config JSON as described in the [Quick Start](#quick-start) section
+* Edit scripts/2P_proc.sh to set paths and options:
+```bash
+# Copy and customize the batch script
+cp scripts/2P_proc_template.sh scripts/2P_proc.sh
+```
+* Run the pipeline
+```bash
+# On a local machine
+bash scripts/2P_proc.sh configs/my_config.json
+# On a cluster with SLURM
+sbatch scripts/2P_proc.sh configs/my_config.json
+```
+The Docker containers are available on [Docker Hub](https://hub.docker.com/r/wanglabneuro/2p_proc). If using Docker, they will be pulled automatically when running the batch script.
+Singularity images can be built from the Docker containers using the provided scripts in `containers/2P_proc/`.
 ## Installation
-### Option 1: Install from GitHub (recommended)
+If you prefer to install the pipeline locally, follow the instructions below.
+### Standard Installation
 ```bash
 # Create and activate conda environment
 conda create -n toupie python=3.10 -c conda-forge # Name the env any name you prefer
 conda activate toupie
-# Install optimouse
-pip install git+https://github.com/vncntprvst/2P-proc.git
+# Install optimouse from PyPI
+pip install optimouse
 # Install CaImAn manager
 caimanmanager install
 ```
-### Option 2: Development install
+### For Developers
 ```bash
 # Clone repository
@@ -88,12 +118,6 @@ caimanmanager install
 ### Additional dependencies
-For z-correction:
-```bash
-conda install -c conda-forge mkl mkl_fft
-pip install suite2p
-```
 For visualization:
 ```bash
 pip install "fastplotlib[notebook]"
@@ -218,14 +242,17 @@ Create a configuration JSON based on `pipeline/configs/config_template_cnmf.json
 **On a local machine:**
 ```bash
-python pipeline/pipeline_mcorr.py configs/my_config.json
-python pipeline/pipeline_cnmf.py configs/my_config.json
+conda activate toupie # Activate your conda environment
+python -m pipeline.pipeline_mcorr configs/my_config.json
+python -m pipeline.pipeline_cnmf configs/my_config.json
 ```
 **On a cluster with SLURM:**
+Copy and customize `scripts/2P_proc_template.sh` to `scripts/2P_proc.sh`, then submit:
 ```bash
-sbatch scripts/batch_2P_pipeline.sh configs/my_config.json
+sbatch scripts/2P_proc.sh configs/my_config.json
 ```
 ### 3. Multi-session registration
@@ -238,13 +265,13 @@ python Caiman/multisession_registration.py --json configs/my_config.json
 ### Motion Correction
 - Rigid and non-rigid motion correction using NoRMCorre algorithm
-- Optional z-drift correction using anatomical z-stack
+- Optional rigid or non-rigid z-drift correction using anatomical z-stack
 - Export to multiple formats (TIFF, memmap, HDF5)
 ### ROI Extraction
-- CNMF (CaImAn): Constrained non-negative matrix factorization with automatic component quality assessment
-- Suite2p: Fast, correlation-based clustering and SVD-accelerated cell detection and extraction
-- Both methods provide denoised fluorescence traces and deconvolved spikes
+- [Option 1] CNMF (CaImAn): Constrained non-negative matrix factorization with automatic component quality assessment
+- [Option 2] Suite2p: Fast, correlation-based clustering and SVD-accelerated cell detection and extraction
+Both methods provide denoised fluorescence traces and deconvolved spikes
 ### ROI Z-Correction
 - Regress and subtract axial drift from ROI traces
@@ -255,10 +282,10 @@ python Caiman/multisession_registration.py --json configs/my_config.json
 Jupyter notebooks in `Mesmerize/` for systematic parameter exploration:
 - `optimize_mcorr_bruker.ipynb`: Motion correction parameters
 - `optimize_cnmf_bruker.ipynb`: CNMF extraction parameters
-- `pipeline_notebook_template.ipynb`: Complete pipeline template
+- `pipeline_notebook_template.ipynb`: Complete pipeline template (**Needs to be updated**)
 ## Testing
+**Note: the tests are outdated and may not reflect the current state of the pipeline.**
 ```bash
 # Download test data (~1.2GB)
 ./scripts/download_test_data.sh
@@ -280,17 +307,17 @@ Docker/Singularity containers are available for cluster computing:
 Build and use containers:
 ```bash
 # Build container
-cd containers/analysis_2p
-docker build -t optimouse:latest .
+cd containers/2P_proc
+./build.sh # For Docker only
+./build_docker_singularity.sh # For Singularity too
 # Run with Singularity
-singularity exec containers/analysis-2p_latest.sif python pipeline/pipeline_mcorr.py config.json
+singularity exec containers/2p_proc_latest.sif python -m pipeline.pipeline_mcorr configs/my_config.json
 ```
 ## Documentation
-- **Configuration**: See `pipeline/configs/config_template_cnmf.json` for all available parameters
-- **API Reference**: Coming soon
+- **Configuration**: See `pipeline/configs/config_template_cnmf.json` and `pipeline/configs/config_template_suite2p.json` for available parameters
 - **Tutorials**: Jupyter notebooks in `Mesmerize/` and `Caiman/`
 ## Post-Processing and Analysis
@@ -308,9 +335,10 @@ Contributions are welcome! Please:
 ## Citation
-If you use this software, please cite:
+This pipeline builds upon the following tools:
 - CaImAn: Giovannucci et al. (2019) eLife
 - Mesmerize: Kolar et al. (2019) Nature Communications
+- Suite2p: Pachitariu et al. (2017) bioRxiv
 ## License

{optimouse-0.1.0 → optimouse-0.1.2}/README.md RENAMED Viewed

@@ -2,32 +2,56 @@
 [![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)](https://www.python.org/)
 [![CaImAn Version](https://img.shields.io/badge/CaImAn-1.12.2+-green)](https://github.com/flatironinstitute/CaImAn)
+[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
+[![DOI](https://zenodo.org/badge/1141473002.svg)](https://doi.org/10.5281/zenodo.18371949)
+<!-- [![Build Status](https://img.shields.io/github/actions/workflow/status/vncntprvst/2P-proc/ci.yml)](https://github.com/vncntprvst/2P-proc/actions) -->
 ![License](https://img.shields.io/badge/license-MIT-red)
-**2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/) and [Mesmerize](https://github.com/nel-lab/mesmerize-core/).
+**2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/), [Mesmerize](https://github.com/nel-lab/mesmerize-core/) and [Suite2p](https://github.com/MouseLand/suite2p).
 This package provides:
-- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction
-- **ROI extraction**: CNMF-based and Suite2p-based cell detection and segmentation
+- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid/non-rigid)
+- **ROI extraction**: CNMF-based or Suite2p-based cell detection and segmentation
 - **Spike deconvolution**: Temporal activity inference from calcium signals
-- **Parameter optimization**: Notebooks for systematic parameter exploration
+- **Parameter optimization**: Notebooks for systematic parameter exploration (CaImAn NoRMCorre and CNMF)
 - **Multi-session registration**: Cross-session ROI alignment using CaImAn's registration algorithm
+## No-installation Quick Start
+Try the pipeline without installation, using containers:
+* Create your config JSON as described in the [Quick Start](#quick-start) section
+* Edit scripts/2P_proc.sh to set paths and options:
+```bash
+# Copy and customize the batch script
+cp scripts/2P_proc_template.sh scripts/2P_proc.sh
+```
+* Run the pipeline
+```bash
+# On a local machine
+bash scripts/2P_proc.sh configs/my_config.json
+# On a cluster with SLURM
+sbatch scripts/2P_proc.sh configs/my_config.json
+```
+The Docker containers are available on [Docker Hub](https://hub.docker.com/r/wanglabneuro/2p_proc). If using Docker, they will be pulled automatically when running the batch script.
+Singularity images can be built from the Docker containers using the provided scripts in `containers/2P_proc/`.
 ## Installation
-### Option 1: Install from GitHub (recommended)
+If you prefer to install the pipeline locally, follow the instructions below.
+### Standard Installation
 ```bash
 # Create and activate conda environment
 conda create -n toupie python=3.10 -c conda-forge # Name the env any name you prefer
 conda activate toupie
-# Install optimouse
-pip install git+https://github.com/vncntprvst/2P-proc.git
+# Install optimouse from PyPI
+pip install optimouse
 # Install CaImAn manager
 caimanmanager install
 ```
-### Option 2: Development install
+### For Developers
 ```bash
 # Clone repository
@@ -47,12 +71,6 @@ caimanmanager install
 ### Additional dependencies
-For z-correction:
-```bash
-conda install -c conda-forge mkl mkl_fft
-pip install suite2p
-```
 For visualization:
 ```bash
 pip install "fastplotlib[notebook]"
@@ -177,14 +195,17 @@ Create a configuration JSON based on `pipeline/configs/config_template_cnmf.json
 **On a local machine:**
 ```bash
-python pipeline/pipeline_mcorr.py configs/my_config.json
-python pipeline/pipeline_cnmf.py configs/my_config.json
+conda activate toupie # Activate your conda environment
+python -m pipeline.pipeline_mcorr configs/my_config.json
+python -m pipeline.pipeline_cnmf configs/my_config.json
 ```
 **On a cluster with SLURM:**
+Copy and customize `scripts/2P_proc_template.sh` to `scripts/2P_proc.sh`, then submit:
 ```bash
-sbatch scripts/batch_2P_pipeline.sh configs/my_config.json
+sbatch scripts/2P_proc.sh configs/my_config.json
 ```
 ### 3. Multi-session registration
@@ -197,13 +218,13 @@ python Caiman/multisession_registration.py --json configs/my_config.json
 ### Motion Correction
 - Rigid and non-rigid motion correction using NoRMCorre algorithm
-- Optional z-drift correction using anatomical z-stack
+- Optional rigid or non-rigid z-drift correction using anatomical z-stack
 - Export to multiple formats (TIFF, memmap, HDF5)
 ### ROI Extraction
-- CNMF (CaImAn): Constrained non-negative matrix factorization with automatic component quality assessment
-- Suite2p: Fast, correlation-based clustering and SVD-accelerated cell detection and extraction
-- Both methods provide denoised fluorescence traces and deconvolved spikes
+- [Option 1] CNMF (CaImAn): Constrained non-negative matrix factorization with automatic component quality assessment
+- [Option 2] Suite2p: Fast, correlation-based clustering and SVD-accelerated cell detection and extraction
+Both methods provide denoised fluorescence traces and deconvolved spikes
 ### ROI Z-Correction
 - Regress and subtract axial drift from ROI traces
@@ -214,10 +235,10 @@ python Caiman/multisession_registration.py --json configs/my_config.json
 Jupyter notebooks in `Mesmerize/` for systematic parameter exploration:
 - `optimize_mcorr_bruker.ipynb`: Motion correction parameters
 - `optimize_cnmf_bruker.ipynb`: CNMF extraction parameters
-- `pipeline_notebook_template.ipynb`: Complete pipeline template
+- `pipeline_notebook_template.ipynb`: Complete pipeline template (**Needs to be updated**)
 ## Testing
+**Note: the tests are outdated and may not reflect the current state of the pipeline.**
 ```bash
 # Download test data (~1.2GB)
 ./scripts/download_test_data.sh
@@ -239,17 +260,17 @@ Docker/Singularity containers are available for cluster computing:
 Build and use containers:
 ```bash
 # Build container
-cd containers/analysis_2p
-docker build -t optimouse:latest .
+cd containers/2P_proc
+./build.sh # For Docker only
+./build_docker_singularity.sh # For Singularity too
 # Run with Singularity
-singularity exec containers/analysis-2p_latest.sif python pipeline/pipeline_mcorr.py config.json
+singularity exec containers/2p_proc_latest.sif python -m pipeline.pipeline_mcorr configs/my_config.json
 ```
 ## Documentation
-- **Configuration**: See `pipeline/configs/config_template_cnmf.json` for all available parameters
-- **API Reference**: Coming soon
+- **Configuration**: See `pipeline/configs/config_template_cnmf.json` and `pipeline/configs/config_template_suite2p.json` for available parameters
 - **Tutorials**: Jupyter notebooks in `Mesmerize/` and `Caiman/`
 ## Post-Processing and Analysis
@@ -267,9 +288,10 @@ Contributions are welcome! Please:
 ## Citation
-If you use this software, please cite:
+This pipeline builds upon the following tools:
 - CaImAn: Giovannucci et al. (2019) eLife
 - Mesmerize: Kolar et al. (2019) Nature Communications
+- Suite2p: Pachitariu et al. (2017) bioRxiv
 ## License

{optimouse-0.1.0 → optimouse-0.1.2}/optimouse.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: optimouse
-Version: 0.1.0
+Version: 0.1.2
 Summary: 2-photon calcium imaging data processing pipeline with CaImAn / Suite2P
 Author-email: Vincent Prevosto <prevosto@mit.edu>, Manuel Levy <levym@mit.edu>
 License-Expression: MIT
@@ -20,7 +20,6 @@ Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: caiman<=1.13.0,>=1.12.2
 Requires-Dist: mesmerize-core>=0.5.0
 Requires-Dist: numpy>=1.26.4
 Requires-Dist: scipy>=1.15.3
@@ -37,38 +36,69 @@ Requires-Dist: ruff>=0.0.200; extra == "dev"
 Provides-Extra: viz
 Requires-Dist: fastplotlib>=0.1.0a16; extra == "viz"
 Requires-Dist: plotly>=6.5.2; extra == "viz"
+Provides-Extra: all
+Requires-Dist: pytest>=7.0.0; extra == "all"
+Requires-Dist: pytest-cov>=3.0.0; extra == "all"
+Requires-Dist: black>=22.0.0; extra == "all"
+Requires-Dist: ruff>=0.0.200; extra == "all"
+Requires-Dist: fastplotlib>=0.1.0a16; extra == "all"
+Requires-Dist: plotly>=6.5.2; extra == "all"
 Dynamic: license-file
 # 2P-proc (optimouse)
 [![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)](https://www.python.org/)
 [![CaImAn Version](https://img.shields.io/badge/CaImAn-1.12.2+-green)](https://github.com/flatironinstitute/CaImAn)
+[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
+[![DOI](https://zenodo.org/badge/1141473002.svg)](https://doi.org/10.5281/zenodo.18371949)
+<!-- [![Build Status](https://img.shields.io/github/actions/workflow/status/vncntprvst/2P-proc/ci.yml)](https://github.com/vncntprvst/2P-proc/actions) -->
 ![License](https://img.shields.io/badge/license-MIT-red)
-**2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/) and [Mesmerize](https://github.com/nel-lab/mesmerize-core/).
+**2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/), [Mesmerize](https://github.com/nel-lab/mesmerize-core/) and [Suite2p](https://github.com/MouseLand/suite2p).
 This package provides:
-- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction
-- **ROI extraction**: CNMF-based and Suite2p-based cell detection and segmentation
+- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid/non-rigid)
+- **ROI extraction**: CNMF-based or Suite2p-based cell detection and segmentation
 - **Spike deconvolution**: Temporal activity inference from calcium signals
-- **Parameter optimization**: Notebooks for systematic parameter exploration
+- **Parameter optimization**: Notebooks for systematic parameter exploration (CaImAn NoRMCorre and CNMF)
 - **Multi-session registration**: Cross-session ROI alignment using CaImAn's registration algorithm
+## No-installation Quick Start
+Try the pipeline without installation, using containers:
+* Create your config JSON as described in the [Quick Start](#quick-start) section
+* Edit scripts/2P_proc.sh to set paths and options:
+```bash
+# Copy and customize the batch script
+cp scripts/2P_proc_template.sh scripts/2P_proc.sh
+```
+* Run the pipeline
+```bash
+# On a local machine
+bash scripts/2P_proc.sh configs/my_config.json
+# On a cluster with SLURM
+sbatch scripts/2P_proc.sh configs/my_config.json
+```
+The Docker containers are available on [Docker Hub](https://hub.docker.com/r/wanglabneuro/2p_proc). If using Docker, they will be pulled automatically when running the batch script.
+Singularity images can be built from the Docker containers using the provided scripts in `containers/2P_proc/`.
 ## Installation
-### Option 1: Install from GitHub (recommended)
+If you prefer to install the pipeline locally, follow the instructions below.
+### Standard Installation
 ```bash
 # Create and activate conda environment
 conda create -n toupie python=3.10 -c conda-forge # Name the env any name you prefer
 conda activate toupie
-# Install optimouse
-pip install git+https://github.com/vncntprvst/2P-proc.git
+# Install optimouse from PyPI
+pip install optimouse
 # Install CaImAn manager
 caimanmanager install
 ```
-### Option 2: Development install
+### For Developers
 ```bash
 # Clone repository
@@ -88,12 +118,6 @@ caimanmanager install
 ### Additional dependencies
-For z-correction:
-```bash
-conda install -c conda-forge mkl mkl_fft
-pip install suite2p
-```
 For visualization:
 ```bash
 pip install "fastplotlib[notebook]"
@@ -218,14 +242,17 @@ Create a configuration JSON based on `pipeline/configs/config_template_cnmf.json
 **On a local machine:**
 ```bash
-python pipeline/pipeline_mcorr.py configs/my_config.json
-python pipeline/pipeline_cnmf.py configs/my_config.json
+conda activate toupie # Activate your conda environment
+python -m pipeline.pipeline_mcorr configs/my_config.json
+python -m pipeline.pipeline_cnmf configs/my_config.json
 ```
 **On a cluster with SLURM:**
+Copy and customize `scripts/2P_proc_template.sh` to `scripts/2P_proc.sh`, then submit:
 ```bash
-sbatch scripts/batch_2P_pipeline.sh configs/my_config.json
+sbatch scripts/2P_proc.sh configs/my_config.json
 ```
 ### 3. Multi-session registration
@@ -238,13 +265,13 @@ python Caiman/multisession_registration.py --json configs/my_config.json
 ### Motion Correction
 - Rigid and non-rigid motion correction using NoRMCorre algorithm
-- Optional z-drift correction using anatomical z-stack
+- Optional rigid or non-rigid z-drift correction using anatomical z-stack
 - Export to multiple formats (TIFF, memmap, HDF5)
 ### ROI Extraction
-- CNMF (CaImAn): Constrained non-negative matrix factorization with automatic component quality assessment
-- Suite2p: Fast, correlation-based clustering and SVD-accelerated cell detection and extraction
-- Both methods provide denoised fluorescence traces and deconvolved spikes
+- [Option 1] CNMF (CaImAn): Constrained non-negative matrix factorization with automatic component quality assessment
+- [Option 2] Suite2p: Fast, correlation-based clustering and SVD-accelerated cell detection and extraction
+Both methods provide denoised fluorescence traces and deconvolved spikes
 ### ROI Z-Correction
 - Regress and subtract axial drift from ROI traces
@@ -255,10 +282,10 @@ python Caiman/multisession_registration.py --json configs/my_config.json
 Jupyter notebooks in `Mesmerize/` for systematic parameter exploration:
 - `optimize_mcorr_bruker.ipynb`: Motion correction parameters
 - `optimize_cnmf_bruker.ipynb`: CNMF extraction parameters
-- `pipeline_notebook_template.ipynb`: Complete pipeline template
+- `pipeline_notebook_template.ipynb`: Complete pipeline template (**Needs to be updated**)
 ## Testing
+**Note: the tests are outdated and may not reflect the current state of the pipeline.**
 ```bash
 # Download test data (~1.2GB)
 ./scripts/download_test_data.sh
@@ -280,17 +307,17 @@ Docker/Singularity containers are available for cluster computing:
 Build and use containers:
 ```bash
 # Build container
-cd containers/analysis_2p
-docker build -t optimouse:latest .
+cd containers/2P_proc
+./build.sh # For Docker only
+./build_docker_singularity.sh # For Singularity too
 # Run with Singularity
-singularity exec containers/analysis-2p_latest.sif python pipeline/pipeline_mcorr.py config.json
+singularity exec containers/2p_proc_latest.sif python -m pipeline.pipeline_mcorr configs/my_config.json
 ```
 ## Documentation
-- **Configuration**: See `pipeline/configs/config_template_cnmf.json` for all available parameters
-- **API Reference**: Coming soon
+- **Configuration**: See `pipeline/configs/config_template_cnmf.json` and `pipeline/configs/config_template_suite2p.json` for available parameters
 - **Tutorials**: Jupyter notebooks in `Mesmerize/` and `Caiman/`
 ## Post-Processing and Analysis
@@ -308,9 +335,10 @@ Contributions are welcome! Please:
 ## Citation
-If you use this software, please cite:
+This pipeline builds upon the following tools:
 - CaImAn: Giovannucci et al. (2019) eLife
 - Mesmerize: Kolar et al. (2019) Nature Communications
+- Suite2p: Pachitariu et al. (2017) bioRxiv
 ## License

{optimouse-0.1.0 → optimouse-0.1.2}/optimouse.egg-info/requires.txt RENAMED Viewed

@@ -1,4 +1,3 @@
-caiman<=1.13.0,>=1.12.2
 mesmerize-core>=0.5.0
 numpy>=1.26.4
 scipy>=1.15.3
@@ -8,6 +7,14 @@ h5py>=3.14.0
 opencv-python>=4.11.0.86
 pylibtiff>=0.7.0
+[all]
+pytest>=7.0.0
+pytest-cov>=3.0.0
+black>=22.0.0
+ruff>=0.0.200
+fastplotlib>=0.1.0a16
+plotly>=6.5.2
 [dev]
 pytest>=7.0.0
 pytest-cov>=3.0.0

{optimouse-0.1.0 → optimouse-0.1.2}/pipeline/configs/config_C57_O1M2_10022023_run1run2.json RENAMED Viewed

@@ -32,7 +32,7 @@
             "/home/wanglab/data/2P/C57_O1M2/10022023/TSeries-10022023-1300-002"
         ],
         "export_paths": [
-            "/home/wanglab/data/2P/Analysis_2P/C57_O1M2/10022023/run1run2/test_spintop"
+            "/home/wanglab/data/2P/Analysis_2P/C57_O1M2/10022023/run1run2/test_optimouse"
         ],
         "zstack_paths": [
             "/home/wanglab/data/2P/C57_O1M2/10022023/ZSeries-10022023-1300-004"

{optimouse-0.1.0 → optimouse-0.1.2}/pipeline/utils/pipeline_utils.py RENAMED Viewed

@@ -187,22 +187,32 @@ def cleanup_files(batch_path, export_path, preserve_batch=False):
             if batch_runfile.exists():
                 batch_runfile.unlink()
             batch_dir = Path(export_path) / batch_id
-        if batch_dir.exists():
-            for attempt in range(3):
-                time.sleep(1 + attempt)
-                try:
-                    shutil.rmtree(batch_dir)
-                    break
-                except Exception as e:
-                    if attempt == 2:
-                        log_and_print(f"Could not delete {batch_dir}: {e}")
+            if batch_dir.exists():
+                for attempt in range(3):
+                    time.sleep(1 + attempt)
+                    try:
+                        shutil.rmtree(batch_dir)
+                        break
+                    except Exception as e:
+                        if attempt == 2:
+                            log_and_print(f"Could not delete {batch_dir}: {e}")
         for pickle_file in Path(export_path).glob("batch_*.pickle"):
             pickle_file.unlink()
+        # Remove mcorr mmap file if preserve_batch is False
+        # (i.e., when output format is not "memmap")
+        for mmap_file in Path(export_path).glob('mcorr_*.mmap'):
+            try:
+                mmap_file.unlink()
+                log_and_print(f"Removed intermediate mmap file: {mmap_file}")
+            except Exception as e:
+                log_and_print(f"Could not remove {mmap_file}: {e}", level="warning")
     # Remove concatenated tiff if present
     cat_tiff_path = Path(export_path) / 'cat_tiff_bt.tiff'
     if cat_tiff_path.exists():
         cat_tiff_path.unlink()
     # NOTE: Do not remove the final motion-corrected movie here.
     # Downstream steps (ops creation and extraction) may rely on
     # `mcorr_movie.*` being present in the export directory.
@@ -233,7 +243,10 @@ def cleanup_files(batch_path, export_path, preserve_batch=False):
                 sc.unlink()
             except Exception:
                 pass
-    log_and_print("Batch files deleted.\n")
+    if not preserve_batch:
+        log_and_print("Batch files deleted.\n")
+    else:
+        log_and_print("Batch files preserved.\n")
 def find_latest_batch(export_path):

{optimouse-0.1.0 → optimouse-0.1.2}/pyproject.toml RENAMED Viewed

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "optimouse"
-version = "0.1.0"
+version = "0.1.2"
 description = "2-photon calcium imaging data processing pipeline with CaImAn / Suite2P"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -27,7 +27,6 @@ classifiers = [
 ]
 dependencies = [
-    "caiman>=1.12.2,<=1.13.0",
     "mesmerize-core>=0.5.0",
     "numpy>=1.26.4",
     "scipy>=1.15.3",
@@ -49,6 +48,18 @@ viz = [
     "fastplotlib>=0.1.0a16",
     "plotly>=6.5.2",
 ]
+all = [
+    "pytest>=7.0.0",
+    "pytest-cov>=3.0.0",
+    "black>=22.0.0",
+    "ruff>=0.0.200",
+    "fastplotlib>=0.1.0a16",
+    "plotly>=6.5.2",
+]
+# Note: CaImAn (>=1.12.2,<1.13.0) must be installed separately from GitHub:
+# uv pip install "git+https://github.com/flatironinstitute/CaImAn.git@v1.12.2"
+# caimanmanager install
 [project.urls]
 Homepage = "https://github.com/vncntprvst/2P-proc"