neuro-sam 0.1.15

Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation

Neuro-SAM

Foundation Model from Dendrite and Dendritic Spine Segmentation

Neuro-SAM enables you to:

• Trace individual dendrite in a 3D stack
• Segment traced dendrites using fine-tuned SAMv2
• Tubular View Analysis of the dendrites
• Segment Dendritic Spines using our custom model

Neuro-SAM works across different imaging modalities including two-photon, confocal and STED microscopy.

🚀 Installation

Neuro-SAM requires Python 3.10+ installed on your machine. It is recommended to use Conda/Miniconda for environment management. You can also use CUDA for GPU based accelerations. Our model are also optimised to use MPS on Apple Silicon (M series chips).

To install Neuro-SAM:

pip install neuro-sam

Downloading models and sample dataset

neuro-sam-download

📊 Usage

# base usage with benchmark dataset
neuro-sam

# using with your own dataset
neuro-sam --image-path /path/to/your/image.tif

🔬 Workflow

1. Configure Voxel Spacing

Set accurate X, Y, Z voxel spacing in the "Path Tracing" tab for proper scaling:

2. Trace Dendritic Paths

• Click waypoints along dendrite structures
• Algorithm automatically finds optimal brightest paths

3. Segment Dendrites

• Load pre-trained SAMv2 dendrite model
• Segment individual path with SAMv2

4. Segment Spines

• Segment Dendritic Spines with our fine tuned model

📬 Contact

• Nipun Arora - [e-mail]
• Munna Singh - [e-mail]

Made with ♥️ at Anki Lab 🧠✨