{"name":"neuro-sam","display_name":"Neuro-SAM","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"neuro-sam.make_widget","title":"Neuro-SAM","python_name":"neuro_sam.napari_utils.main_widget:NeuroSAMWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"neuro-sam.make_widget","display_name":"Neuro-SAM","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"neuro-sam","version":"0.1.17","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Neuro-SAM: Foundation Model for Dendrite and Dendritic Spine Segmentation","description":"\n\n# Neuro-SAM \n#### Foundation Model from Dendrite and Dendritic Spine Segmentation\n\n
\n\nNeuro-SAM enables you to:\n- Trace individual dendrite in a 3D stack\n- Segment traced dendrites using fine-tuned SAMv2\n- Tubular View Analysis of the dendrites \n- Segment Dendritic Spines using our custom model\n\nNeuro-SAM works across different imaging modalities including two-photon, confocal and STED microscopy.\n\n### 🚀 Installation\n\nNeuro-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). \n\nTo install Neuro-SAM: \n\n```bash\npip install neuro-sam\n```\n\nDownloading models and sample dataset\n\n```bash\nneuro-sam-download\n```\n\n### 📊 Usage\n\n```bash\n# base usage with benchmark dataset\nneuro-sam\n\n# using with your own dataset\nneuro-sam --image-path /path/to/your/image.tif\n```\n\n### 🔬 Workflow\n\n#### 1. **Configure Voxel Spacing**\nSet accurate X, Y, Z voxel spacing in the \"Path Tracing\" tab for proper scaling:\n\n#### 2. **Trace Dendritic Paths**\n- Click waypoints along dendrite structures\n- Algorithm automatically finds optimal brightest paths\n\n#### 3. **Segment Dendrites**\n- Load pre-trained SAMv2 dendrite model\n- Segment individual path with SAMv2\n\n#### 4. **Segment Spines**\n- Segment Dendritic Spines with our fine tuned model\n\n### 📬 Contact\n\n- Nipun Arora - nipunarora8@yahoo.com\n- Munna Singh - singhmunna0786@gmail.com\n\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Nipun Arora , Munna Singh ","maintainer":null,"maintainer_email":null,"license":"MIT License\n\nCopyright (c) 2024 Nipun Arora\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n","classifier":["Programming Language :: Python :: 3","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Framework :: napari"],"requires_dist":["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","numba","PyQt5","opencv-python-headless","matplotlib","requests","flammkuchen","albumentations","wandb","tensorflow","imagecodecs"],"requires_python":">=3.10","requires_external":null,"project_url":["Homepage, https://github.com/nipunarora8/Neuro-SAM","Bug Tracker, https://github.com/nipunarora8/Neuro-SAM/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}