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jdeschamps authored Feb 12, 2024
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Expand Up @@ -186,10 +186,10 @@ you to look in [OC project 52](https://github.com/ai4life-opencalls/oc_1_project
[napari-sam-labeling-tools](https://github.com/juglab/napari-sam-labeling-tools) for
how to proceed with this method.

Note that in this case, the goal is still to create masks for the areas we want to
exclude!
> **Note** that in this case, the goal is still to create masks for the areas we want to
> exclude!

There are two pipelines: SAM-RF and SAM with prompts.
**There are two pipelines: SAM-RF and SAM with prompts.**

#### Pre-requisite

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<img src='imgs/2c_manual_label_with_labkit.png' width='600'>
</p>

Note that for the next sections, the normalized images and their corresponding masks
must have the same name, e.g. `raw-normalised/image1.tiff` and `masks/image1.tiff`.
Therefore, you might have to rename the images, for instance by exporting the stack
as a sequence as well.
> Note that for the next sections, the normalized images and their corresponding masks
> must have the same name, e.g. `raw-normalised/image1.tiff` and `masks/image1.tiff`.
> Therefore, you might have to rename the images, for instance by exporting the stack
> as a sequence as well.

We recommend to perform a quality control to check whether the masks are correct. For this,
you can either open all images in Fiji and compare them, or used the
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