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@@ -10,8 +10,42 @@ Our goal is to build fast and interactive annotation tools for microscopy data,
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![box-prompts](https://github.com/computational-cell-analytics/micro-sam/assets/4263537/d04cb158-9f5b-4460-98cd-023c4f19cccd)
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Beta version, Roadmap etc.
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`micro_sam` is under active development, but our goal is to keep the changes to the user interface and the interface of the python library as small as possible.
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On our roadmap for more functionality are:
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- Providing an installer for running `micro_sam` as a standalone application.
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- Releasing more and better finetuned models as well as the code for fine-tuning.
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- Integration of the finetuned models with [bioimage.io](https://bioimage.io/#/)
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- Implementing a napari plugin for `micro_sam`.
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<!----
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Better instance segmentation, Few-shot adapation (using LORA, QLORA, etc.)
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---->
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## Quickstart
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You can install `micro_sam` via conda:
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```
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$ conda install -c conda-forge micro_sam
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```
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For more installation options check out [Installation](#installation)
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After installing `micro_sam` you can run the annotation tool via `$ micro_sam.annotator`, which opens a menu for selecting the annotation tool and its inputs.
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See [Annotation Tools](#annotation-tools) for an overview and explanation of the annotation functionality.
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The `micro_sam` python library can be used via
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```python
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import micro_sam
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```
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It is explained in more detail [here](#how-to-use-the-python-library).
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Our support for finetuned models is still experimental. We will soon release better finetuned models and host them on zenodo.
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For now, check out [the example script for the 2d annotator](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_2d.py#L62) to see how the finetuned models can be used within `micro_sam`.
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## Citation
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If you are using `micro_sam` 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](https://doi.org/10.5281/zenodo.7919746)
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We will release a preprint soon that describes this work and can be cited instead of zenodo.

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