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You can then start the `micro_sam` tools by running `$ micro_sam.annotator` in the command line.
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For an introduction in how to use the napari based annotation tools check out [the video tutorials](https://www.youtube.com/watch?v=ket7bDUP9tI&list=PLwYZXQJ3f36GQPpKCrSbHjGiH39X4XjSO&pp=gAQBiAQB).
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Please check out [the documentation](https://computational-cell-analytics.github.io/micro-sam/) for more details on the installation and usage of `micro_sam`.
Copy file name to clipboardExpand all lines: doc/annotation_tools.md
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@@ -13,9 +13,13 @@ The annotation tools can be started from the `micro_sam` GUI, the command line o
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$ micro_sam.annotator
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```
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They are built with[napari](https://napari.org/stable/) to implement the viewer and user interaction.
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They are built using[napari](https://napari.org/stable/)and [magicgui](https://pyapp-kit.github.io/magicgui/)to provide the viewer and user interface.
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If you are not familiar with napari yet, [start here](https://napari.org/stable/tutorials/fundamentals/quick_start.html).
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The `micro_sam` applications are mainly based on [the point layer](https://napari.org/stable/howtos/layers/points.html), [the shape layer](https://napari.org/stable/howtos/layers/shapes.html) and [the label layer](https://napari.org/stable/howtos/layers/labels.html).
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The `micro_sam` tools use [the point layer](https://napari.org/stable/howtos/layers/points.html), [shape layer](https://napari.org/stable/howtos/layers/shapes.html) and [label layer](https://napari.org/stable/howtos/layers/labels.html).
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The annotation tools are explained in detail below. In addition to the documentation we provide [video tutorials](https://www.youtube.com/watch?v=ket7bDUP9tI&list=PLwYZXQJ3f36GQPpKCrSbHjGiH39X4XjSO) for the tools.
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## Annotator 2D
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Note that point prompts and box prompts can be combined. When you're using point prompts you can only segment one object at a time. With box prompts you can segment several objects at once.
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Check out [this video](https://youtu.be/DfWE_XRcqN8) for an example of how to use the interactive 2d annotator.
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Check out [this video](https://youtu.be/ket7bDUP9tI) for a tutorial for the 2d annotation tool.
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We also provide the `image series annotator`, which can be used for running the 2d annotator for several images in a folder. You can start by clicking `Image series annotator` in the GUI, running `micro_sam.image_series_annotator` in the command line or from a [python script](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/image_series_annotator.py).
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Note that you can only segment one object at a time with the 3d annotator.
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Check out [this video](https://youtu.be/5Jo_CtIefTM) for an overview of the interactive 3d segmentation functionality.
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Check out [this video](https://youtu.be/PEy9-rTCdS4) for a tutorial for the 3d annotation tool.
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## Annotator Tracking
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Note that the tracking annotator only supports 2d image data, volumetric data is not supported.
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Check out [this video](https://youtu.be/PBPW0rDOn9w) for an overview of the interactive tracking functionality.
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Check out [this video](https://youtu.be/Xi5pRWMO6_w) for a tutorial for how to use the tracking annotation tool.
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