neuro-sam 0.1.0__tar.gz

neuro_sam-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Nipun Arora
+
+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.

neuro_sam-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: neuro-sam
+Version: 0.1.0
+Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
+Author-email: Nipun Arora <nipun.arora@fau.de>
+License: MIT License
+        
+        Copyright (c) 2024 Nipun Arora
+        
+        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/nipunarora8/Neuro-SAM
+Project-URL: Bug Tracker, https://github.com/nipunarora8/Neuro-SAM/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Framework :: napari
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: napari
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: imageio
+Requires-Dist: torch>=2.0.0
+Requires-Dist: torchvision>=0.15.0
+Requires-Dist: hydra-core>=1.3.2
+Requires-Dist: iopath>=0.1.10
+Requires-Dist: pillow>=9.4.0
+Requires-Dist: tqdm>=4.66.1
+Requires-Dist: vispy
+Requires-Dist: qtpy
+Requires-Dist: superqt
+Requires-Dist: magicgui
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Dynamic: license-file
+
+<div align="center">
+
+# Neuro-SAM 
+#### Foundation Models from Dendrite and Dendritic Spine Segmentation
+
+[![python](https://img.shields.io/badge/-Python_3.10-blue?logo=python&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![pytorch](https://img.shields.io/badge/PyTorch_2.0+-ee4c2c?logo=pytorch&logoColor=white)](https://pytorch.org/get-started/locally/)
+[![wandb](https://img.shields.io/badge/Weights_&_Biases-FFCC33?logo=WeightsAndBiases&logoColor=black)](https://wandb.ai/site)
+
+This project demonstrates an interactive UI to segment dendrites and dendritic spines.
+The model of choice is SAMv2 and the framework used is pytorch.
+
+![A stack of neural dendrites and dendritic spines](./assets/merged_dendrites_spines.gif "Dendrites and Dendritic Spines")
+
+</div>
+
+### 📝  Table of Contents
+
+- [Neuro-SAM](#neuro-sam)
+  - [📑 Table of Contents](#--table-of-contents)
+  - [🧠 Overview](#-overview)
+  - [📦 Built With](#-built-with)
+  - [📂 Repository Structure](#-repository-structure)
+  - [🚀 Installation](#-installation)
+  - [📊 Usage](#-usage)
+  - [🛠 Workflow](#-workflow)
+  - [🧑‍💻 Model Training](#-model-training)
+  - [📁 Data Format](#-data-format)
+  - [📄 License](#-license)
+  - [📬 Contact](#-contact)
+
+
+### 🧠 Overview
+
+Neuro-SAM provides an end-to-end pipeline for analyzing neural structures from 3D microscopy data, featuring:
+
+- **Path Tracing**: Waypoint-based A* pathfinding
+- **Dendrite Segmentation**: SAM2-based dendrite segmentation
+- **Smart Spine Detection**: Multi-view analysis for spine detection
+- **Spine Segmentation**: Individual spine segmentation using trained SAM2 model
+
+### 📦 Built With
+
+[PyTorch](https://pytorch.org) - an open-source machine learning library for Python, widely used for deep learning applications.
+
+[Segment Anything Model](https://segment-anything.com) - a foundation model used for segmentation built by Meta AI.
+
+[Weights and Biases](https://wandb.ai/site) - a tool for tracking and visualizing machine learning experiments.
+
+[Visual Studio Code](https://code.visualstudio.com/) - a code editor redefined and optimized for building applications.
+
+[FAU High Performance Computing](https://doc.nhr.fau.de/) - a high-performance computing cluster at Friedrich-Alexander-Universität Erlangen-Nürnberg.
+
+### 📁 Repository Structure
+
+```
+Neuro-SAM/
+├── Train-SAMv2/                    # SAM2 training infrastructure
+│   ├── sam2/                       # SAM2 model implementation
+│   ├── checkpoints/                # Model checkpoints
+│   ├── results/                    # Trained model outputs
+│   ├── utils/                      # Training utilities
+│   ├── train_dendrites.py         # Dendrite model training
+│   └── train_spines.py            # Spine model training
+├── brightest_path_lib/             # Advanced pathfinding algorithms
+│   ├── algorithm/                  # A* and waypoint search implementations
+│   ├── cost/                       # Cost function definitions
+│   ├── heuristic/                  # Heuristic functions
+│   ├── visualization/              # Path visualization tools
+│   └── ...
+├── napari_utils/                   # Napari plugin components
+│   ├── main_widget.py             # Main interface with anisotropic scaling
+│   ├── path_tracing_module.py     # Interactive path tracing
+│   ├── segmentation_module.py     # Dendrite segmentation interface
+│   ├── spine_detection_module.py  # Spine detection with smart tracking
+│   ├── spine_segmentation_module.py # Individual spine segmentation
+│   └── visualization_module.py    # Path management and visualization
+└── neuro_sam_plugin.py            # Main plugin entry point
+```
+
+### 🚀 Installation
+
+#### Prerequisites
+
+- Python 3.10+
+- CUDA-compatible GPU (recommended)
+- Conda/Miniconda
+
+#### Environment Setup
+
+1. **Clone the repository:**
+```bash
+git clone https://github.com/nipunarora8/Neuro-SAM.git
+cd Neuro-SAM
+```
+
+2. **Create local environment:**
+```bash
+conda create -p ./.venv python=3.10 -c conda-forge
+conda activate ./.venv
+```
+
+3. **Install dependencies:**
+```bash
+pip install uv
+uv sync
+```
+
+4. **Download SAM2 checkpoints:**
+```bash
+cd Train-SAMv2/checkpoints
+bash download_ckpts.sh
+```
+
+### 📊 Usage
+
+#### Quick Start
+
+```python
+from neuro_sam_plugin import run_neuro_sam
+
+# Launch with default spacing (94nm x 94nm x 500nm)
+viewer = run_neuro_sam(image_path="your_image.tif")
+
+# Launch with custom voxel spacing
+viewer = run_neuro_sam(
+    image_path="your_image.tif",
+    spacing_xyz=(100.0, 100.0, 300.0)  # X, Y, Z spacing in nm
+)
+```
+
+#### Command Line Interface
+
+```bash
+# Basic usage
+python neuro_sam_plugin.py --image_path /path/to/your/image.tif
+
+# Custom spacing
+python neuro_sam_plugin.py --image_path image.tif \
+    --x-spacing 100.0 --y-spacing 100.0 --z-spacing 300.0
+
+# Load benchmark dataset
+python neuro_sam_plugin.py
+```
+
+### 🔬 Workflow
+
+#### 1. **Configure Voxel Spacing**
+Set accurate X, Y, Z voxel spacing in the "Path Tracing" tab for proper anisotropic scaling:
+- Typical two-photon: 94nm × 94nm × 500nm
+- Confocal: varies by objective and zoom
+
+#### 2. **Trace Dendritic Paths**
+- Click waypoints along dendrite structures
+- Algorithm automatically finds optimal brightess paths
+
+#### 3. **Segment Dendrites**
+- Load pre-trained SAMv2 dendrite model
+- Segment individual path with SAMv2
+
+#### 4. **Detect Spines**
+- Smart multi-view detection using tube data generation
+- Angle-based matching between 2D and tubular views
+
+#### 5. **Segment Spines**
+- Fine-grained spine segmentation using specialized SAMv2 model
+- Dendrite mask overlay to suppress background signal
+- Manual point extension across frames
+- Contrasting color system for visualization
+
+### 🔧 Model Training
+
+#### Dendrite Model
+```bash
+cd Train-SAMv2
+python train_dendrites.py --ppn 20 --pnn 10 --batch_size 32 --model_name "small"
+```
+
+#### Spine Model  
+```bash
+python train_spines.py --model_name "small" --batch_size 16
+```
+
+### 📁 Data Format
+
+#### Input Requirements
+- **Image Format**: TIFF, .d3set (to reproduce training results)
+- **Dimensions**: 3D volumes (Z×Y×X) 
+- **Bit Depth**: 8-bit or 16-bit grayscale
+- **Size**: Tested up to 2048×2048×500 voxels
+
+#### Output Formats
+- **Paths**: NumPy arrays with coordinates
+- **Masks**: Binary TIFF volumes
+
+### 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+
+#### Useful VSCode Extensions
+
+- [Remote Explorer](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-explorer) - Open projects on remote servers.
+- [Log Viewer](https://marketplace.visualstudio.com/items?itemName=berublan.vscode-log-viewer) - A log monitoring extension.
+- [Black Formatter](https://marketplace.visualstudio.com/items?itemName=ms-python.black-formatter) - Python auto code formatter.
+- [Markdown All in One](https://marketplace.visualstudio.com/items?itemName=yzhang.markdown-all-in-one) - Markdown preview and editing.
+
+### 📬  Contact
+
+Nipun Arora - nipun.arora@fau.de
+
+---
+<div align="center">
+<b>Made with ♥️ at Anki Lab 🧠✨</b>
+</div>

neuro_sam-0.1.0/README.md

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+<div align="center">
+
+# Neuro-SAM 
+#### Foundation Models from Dendrite and Dendritic Spine Segmentation
+
+[![python](https://img.shields.io/badge/-Python_3.10-blue?logo=python&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![pytorch](https://img.shields.io/badge/PyTorch_2.0+-ee4c2c?logo=pytorch&logoColor=white)](https://pytorch.org/get-started/locally/)
+[![wandb](https://img.shields.io/badge/Weights_&_Biases-FFCC33?logo=WeightsAndBiases&logoColor=black)](https://wandb.ai/site)
+
+This project demonstrates an interactive UI to segment dendrites and dendritic spines.
+The model of choice is SAMv2 and the framework used is pytorch.
+
+![A stack of neural dendrites and dendritic spines](./assets/merged_dendrites_spines.gif "Dendrites and Dendritic Spines")
+
+</div>
+
+### 📝  Table of Contents
+
+- [Neuro-SAM](#neuro-sam)
+  - [📑 Table of Contents](#--table-of-contents)
+  - [🧠 Overview](#-overview)
+  - [📦 Built With](#-built-with)
+  - [📂 Repository Structure](#-repository-structure)
+  - [🚀 Installation](#-installation)
+  - [📊 Usage](#-usage)
+  - [🛠 Workflow](#-workflow)
+  - [🧑‍💻 Model Training](#-model-training)
+  - [📁 Data Format](#-data-format)
+  - [📄 License](#-license)
+  - [📬 Contact](#-contact)
+
+
+### 🧠 Overview
+
+Neuro-SAM provides an end-to-end pipeline for analyzing neural structures from 3D microscopy data, featuring:
+
+- **Path Tracing**: Waypoint-based A* pathfinding
+- **Dendrite Segmentation**: SAM2-based dendrite segmentation
+- **Smart Spine Detection**: Multi-view analysis for spine detection
+- **Spine Segmentation**: Individual spine segmentation using trained SAM2 model
+
+### 📦 Built With
+
+[PyTorch](https://pytorch.org) - an open-source machine learning library for Python, widely used for deep learning applications.
+
+[Segment Anything Model](https://segment-anything.com) - a foundation model used for segmentation built by Meta AI.
+
+[Weights and Biases](https://wandb.ai/site) - a tool for tracking and visualizing machine learning experiments.
+
+[Visual Studio Code](https://code.visualstudio.com/) - a code editor redefined and optimized for building applications.
+
+[FAU High Performance Computing](https://doc.nhr.fau.de/) - a high-performance computing cluster at Friedrich-Alexander-Universität Erlangen-Nürnberg.
+
+### 📁 Repository Structure
+
+```
+Neuro-SAM/
+├── Train-SAMv2/                    # SAM2 training infrastructure
+│   ├── sam2/                       # SAM2 model implementation
+│   ├── checkpoints/                # Model checkpoints
+│   ├── results/                    # Trained model outputs
+│   ├── utils/                      # Training utilities
+│   ├── train_dendrites.py         # Dendrite model training
+│   └── train_spines.py            # Spine model training
+├── brightest_path_lib/             # Advanced pathfinding algorithms
+│   ├── algorithm/                  # A* and waypoint search implementations
+│   ├── cost/                       # Cost function definitions
+│   ├── heuristic/                  # Heuristic functions
+│   ├── visualization/              # Path visualization tools
+│   └── ...
+├── napari_utils/                   # Napari plugin components
+│   ├── main_widget.py             # Main interface with anisotropic scaling
+│   ├── path_tracing_module.py     # Interactive path tracing
+│   ├── segmentation_module.py     # Dendrite segmentation interface
+│   ├── spine_detection_module.py  # Spine detection with smart tracking
+│   ├── spine_segmentation_module.py # Individual spine segmentation
+│   └── visualization_module.py    # Path management and visualization
+└── neuro_sam_plugin.py            # Main plugin entry point
+```
+
+### 🚀 Installation
+
+#### Prerequisites
+
+- Python 3.10+
+- CUDA-compatible GPU (recommended)
+- Conda/Miniconda
+
+#### Environment Setup
+
+1. **Clone the repository:**
+```bash
+git clone https://github.com/nipunarora8/Neuro-SAM.git
+cd Neuro-SAM
+```
+
+2. **Create local environment:**
+```bash
+conda create -p ./.venv python=3.10 -c conda-forge
+conda activate ./.venv
+```
+
+3. **Install dependencies:**
+```bash
+pip install uv
+uv sync
+```
+
+4. **Download SAM2 checkpoints:**
+```bash
+cd Train-SAMv2/checkpoints
+bash download_ckpts.sh
+```
+
+### 📊 Usage
+
+#### Quick Start
+
+```python
+from neuro_sam_plugin import run_neuro_sam
+
+# Launch with default spacing (94nm x 94nm x 500nm)
+viewer = run_neuro_sam(image_path="your_image.tif")
+
+# Launch with custom voxel spacing
+viewer = run_neuro_sam(
+    image_path="your_image.tif",
+    spacing_xyz=(100.0, 100.0, 300.0)  # X, Y, Z spacing in nm
+)
+```
+
+#### Command Line Interface
+
+```bash
+# Basic usage
+python neuro_sam_plugin.py --image_path /path/to/your/image.tif
+
+# Custom spacing
+python neuro_sam_plugin.py --image_path image.tif \
+    --x-spacing 100.0 --y-spacing 100.0 --z-spacing 300.0
+
+# Load benchmark dataset
+python neuro_sam_plugin.py
+```
+
+### 🔬 Workflow
+
+#### 1. **Configure Voxel Spacing**
+Set accurate X, Y, Z voxel spacing in the "Path Tracing" tab for proper anisotropic scaling:
+- Typical two-photon: 94nm × 94nm × 500nm
+- Confocal: varies by objective and zoom
+
+#### 2. **Trace Dendritic Paths**
+- Click waypoints along dendrite structures
+- Algorithm automatically finds optimal brightess paths
+
+#### 3. **Segment Dendrites**
+- Load pre-trained SAMv2 dendrite model
+- Segment individual path with SAMv2
+
+#### 4. **Detect Spines**
+- Smart multi-view detection using tube data generation
+- Angle-based matching between 2D and tubular views
+
+#### 5. **Segment Spines**
+- Fine-grained spine segmentation using specialized SAMv2 model
+- Dendrite mask overlay to suppress background signal
+- Manual point extension across frames
+- Contrasting color system for visualization
+
+### 🔧 Model Training
+
+#### Dendrite Model
+```bash
+cd Train-SAMv2
+python train_dendrites.py --ppn 20 --pnn 10 --batch_size 32 --model_name "small"
+```
+
+#### Spine Model  
+```bash
+python train_spines.py --model_name "small" --batch_size 16
+```
+
+### 📁 Data Format
+
+#### Input Requirements
+- **Image Format**: TIFF, .d3set (to reproduce training results)
+- **Dimensions**: 3D volumes (Z×Y×X) 
+- **Bit Depth**: 8-bit or 16-bit grayscale
+- **Size**: Tested up to 2048×2048×500 voxels
+
+#### Output Formats
+- **Paths**: NumPy arrays with coordinates
+- **Masks**: Binary TIFF volumes
+
+### 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+
+#### Useful VSCode Extensions
+
+- [Remote Explorer](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-explorer) - Open projects on remote servers.
+- [Log Viewer](https://marketplace.visualstudio.com/items?itemName=berublan.vscode-log-viewer) - A log monitoring extension.
+- [Black Formatter](https://marketplace.visualstudio.com/items?itemName=ms-python.black-formatter) - Python auto code formatter.
+- [Markdown All in One](https://marketplace.visualstudio.com/items?itemName=yzhang.markdown-all-in-one) - Markdown preview and editing.
+
+### 📬  Contact
+
+Nipun Arora - nipun.arora@fau.de
+
+---
+<div align="center">
+<b>Made with ♥️ at Anki Lab 🧠✨</b>
+</div>

neuro_sam-0.1.0/pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "neuro-sam"
+version = "0.1.0"
+description = "Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation"
+readme = "README.md"
+authors = [
+  { name = "Nipun Arora", email = "nipun.arora@fau.de" },
+]
+license = { file = "LICENSE" }
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Framework :: napari",
+]
+dependencies = [
+    "napari",
+    "numpy",
+    "scipy",
+    "imageio",
+    "torch>=2.0.0",
+    "torchvision>=0.15.0",
+    "hydra-core>=1.3.2",
+    "iopath>=0.1.10",
+    "pillow>=9.4.0",
+    "tqdm>=4.66.1",
+    "vispy",
+    "qtpy",
+    "superqt",
+    "magicgui",
+    "scikit-image",
+    "tifffile"
+]
+requires-python = ">=3.10"
+
+[project.urls]
+"Homepage" = "https://github.com/nipunarora8/Neuro-SAM"
+"Bug Tracker" = "https://github.com/nipunarora8/Neuro-SAM/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["neuro_sam*", "sam2*"]
+
+[tool.setuptools.package-data]
+"sam2" = ["*.yaml", "configs/**/*.yaml"]
+"neuro_sam" = ["napari.yaml"]
+
+[project.entry-points."napari.manifest"]
+neuro-sam = "neuro_sam:napari.yaml"
+
+[tool.uv]
+package = true

neuro_sam-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

neuro_sam-0.1.0/src/neuro_sam/__init__.py

@@ -0,0 +1 @@
+from .plugin import run_neuro_sam

neuro_sam-0.1.0/src/neuro_sam/brightest_path_lib/__init__.py

@@ -0,0 +1,5 @@
+# DO_TRANSONIC = False
+
+# __version__ = "1.0.27"
+# from ._version import __version__
+# from ._myVersion import __version__

neuro_sam-0.1.0/src/neuro_sam/brightest_path_lib/algorithm/__init__.py

@@ -0,0 +1,3 @@
+from .astar import BidirectionalAStarSearch
+from .waypointastar import WaypointBidirectionalAStarSearch
+from .waypointastar_speedup import quick_accurate_optimized_search