-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathnapari-SAMV2.json
102 lines (102 loc) · 7.3 KB
/
napari-SAMV2.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
{
"name": "napari-SAMV2",
"display_name": "Segment Anything V2",
"visibility": "public",
"icon": "",
"categories": [
"Annotation",
"Segmentation"
],
"schema_version": "0.2.1",
"on_activate": null,
"on_deactivate": null,
"contributions": {
"commands": [
{
"id": "napari-SAMV2.make_qwidget",
"title": "SAM V2 plugin",
"python_name": "napari_samv2:SAMV2_min",
"short_title": null,
"category": null,
"icon": null,
"enablement": null
}
],
"readers": null,
"writers": null,
"widgets": [
{
"command": "napari-SAMV2.make_qwidget",
"display_name": "SAMV2",
"autogenerate": false
}
],
"sample_data": null,
"themes": null,
"menus": {},
"submenus": null,
"keybindings": null,
"configuration": []
},
"package_metadata": {
"metadata_version": "2.1",
"name": "napari-SAMV2",
"version": "0.0.5",
"dynamic": null,
"platform": null,
"supported_platform": null,
"summary": "Napari plugin for segment anything version 2 model from meta. Plugin primarily useful for segmenting 3d volumetric data or 3d time series data. ",
"description": "# napari-SAMV2\n\nNapari plugin to use segment anything version 2 models from Meta.\n\nPlugin primarily made for segmenting 3d volumetric data or 3d time series data.\n\n----------------------------------\n\n\n## Installation\n\nPre-requisite of samv2 installation needed: --- Our current plugin supports only sam v 2.0 not 2.1. So, we need to pull the SAM repo around september 15 ,2024 (last update of SAM2.0)\n\n git clone https://github.com/facebookresearch/segment-anything-2.git\n cd segment-anything-2\n git rev-list -n 1 --before=\"2024-09-15\" HEAD\n git checkout <commit_hash>\n pip install -e .\n\nYou can install `napari-SAMV2` via [pip]:\n\n pip install napari-SAMV2\n\n******\n\nThe plugin and installation tested with python 3.10 in conda environment with pytorch-cuda=12.1\n\nconda environment with example :\n\n conda create -n samv2_env python=3.10\n conda activate samv2_env\n conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia\n python -m pip install \"napari[all]\"\n\n git clone https://github.com/facebookresearch/segment-anything-2.git\n cd segment-anything-2\n git rev-list -n 1 --before=\"2024-09-15\" HEAD\n \n git checkout <commit_hash>\n pip install -e .\n pip install napari-SAMV2 \n\n*****\n\n## Usage\n\nMiddle mouse click - positive point\n\nCtrl + Middle mouse click - negative point\n\nTime Series Segmentation :\n\n![samv2_time_series_demo](https://github.com/user-attachments/assets/078ca2bb-3016-4257-ac7c-c3cde8f9d125)\n\n\n\nVolume Segmentation :\n\n![samv2_volume_segmentation](https://github.com/user-attachments/assets/af05fcc4-a60d-44e8-ae05-70764d96e828)\n\n\n\nReference :\n\nExample Data from in demo videos from,\nCell tracking challenge - https://celltrackingchallenge.net/ \nFlyEM project - https://www.janelia.org/project-team/flyem/hemibrain\n\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-SAMV2\" is free and open source software\n\n\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/Krishvraman/napari-SAMV2/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n",
"description_content_type": "text/markdown",
"keywords": null,
"home_page": null,
"download_url": null,
"author": "Krishnan Venkataraman",
"author_email": "[email protected]",
"maintainer": null,
"maintainer_email": null,
"license": "\nCopyright (c) 2024, Krishnan Venkataraman\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n this list of conditions and the following disclaimer in the documentation\n and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n contributors may be used to endorse or promote products derived from\n this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n",
"classifier": [
"Development Status :: 2 - Pre-Alpha",
"Framework :: napari",
"Intended Audience :: Developers",
"License :: OSI Approved :: BSD License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Image Processing"
],
"requires_dist": [
"numpy",
"magicgui",
"qtpy",
"scikit-image",
"tox; extra == \"testing\"",
"pytest; extra == \"testing\"",
"pytest-cov; extra == \"testing\"",
"pytest-qt; extra == \"testing\"",
"napari; extra == \"testing\"",
"pyqt5; extra == \"testing\"",
"numpy; extra == \"testing\""
],
"requires_python": ">=3.9",
"requires_external": null,
"project_url": [
"Bug Tracker, https://github.com/Krishvraman/napari-SAMV2/issues",
"Documentation, https://github.com/Krishvraman/napari-SAMV2#README.md",
"Source Code, https://github.com/Krishvraman/napari-SAMV2",
"User Support, https://github.com/Krishvraman/napari-SAMV2/issues"
],
"provides_extra": [
"testing"
],
"provides_dist": null,
"obsoletes_dist": null
},
"npe1_shim": false
}