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README.md

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## Usage
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After the installation the three applications for interactive annotations can be started from the command line or within a python script:
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- **2d annotation**: via the command `micro_sam.annotator_2d` or with the function `micro_sam.sam_annotator.annotator_2d` from python. Run `micro_sam.annotator_2d -h` or check out [examples/sam_annotator_2d](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_2d.py) for details.
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- **3d annotation**: via the command `micro_sam.annotator_3d` or with the function `micro_sam.sam_annotator.annotator_3d` from python. Run `micro_sam.annotator_3d -h` or check out [examples/sam_annotator_3d](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_3d.py) for details.
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- **2d segmentation**: via the command `micro_sam.annotator_2d` or with the function `micro_sam.sam_annotator.annotator_2d` from python. Run `micro_sam.annotator_2d -h` or check out [examples/sam_annotator_2d](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_2d.py) for details.
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- **3d segmentation**: via the command `micro_sam.annotator_3d` or with the function `micro_sam.sam_annotator.annotator_3d` from python. Run `micro_sam.annotator_3d -h` or check out [examples/sam_annotator_3d](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_3d.py) for details.
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- **tracking**: via the command `micro_sam.annotator_tracking` or with the function `micro_sam.sam_annotator.annotator_tracking` from python. Run `micro_sam.annotator_tracking -h` or check out [examples/sam_annotator_tracking](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_tracking.py) for details.
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If you are using this repository in your research please cite
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- [SegmentAnything](https://arxiv.org/abs/2304.02643)
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- and our repository on [zenodo](TODO) (we are working on a full publication)
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- and our repository on [zenodo](TODO) (we are working on a publication)

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