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Correct misnamed functions containing "_rb" in README
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tsipkens authored May 7, 2024
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Expand Up @@ -234,17 +234,17 @@ This `seg_carboseg(...)` function employs Python to implement a convolutional ne
Details on the setup and use of this component are given in the [README](carboseg/README.md) in the **carboseg** subfolder. Two options exist for interacting with the Python code: (1) initializing an instance of Python directly in MATLAB or (2) a multi-step procedure of exporting and reimporting images.


### + **seg_otsu_rb\*** / Otsu thresholding
### + **seg_otsu\*** / Otsu thresholding

These automated methods apply Otsu thresholding followed by a rolling ball transformation. Two versions of this function are included.

**A.** The `agg.seg_otsu_rb_orig(...)` function remains more true to the original code of [Dastanpour et al. (2016)][dastanpour2016]. For the sample images, this often results in fragmented segmentations, e.g.,
**A.** The `agg.seg_otsu_orig(...)` function remains more true to the original code of [Dastanpour et al. (2016)][dastanpour2016]. For the sample images, this often results in fragmented segmentations, e.g.,

![rb_orig](docs/otsu_rb_orig.png)

As the technique may be insufficient on its own, this implementation can be complimented with `agg.seg_slider(...)`, described [below](#-seg_slider_orig--gui-based-slider-method), to fill in the gaps between the aggregates and add missing aggregates.

**B.** Stemming from the deficiencies of the above function, the `agg.seg_otsu_rb(...)` function updates the above implementation by (*i*) not immediately removing boundary aggregates, (*ii*) adding a background subtraction step using the `agg.bg_subtract(...)` function, and (*iii*) adding a bilateral denoising step. This results in the following segmentations.
**B.** Stemming from the deficiencies of the above function, the `agg.seg_otsu(...)` function updates the above implementation by (*i*) not immediately removing boundary aggregates, (*ii*) adding a background subtraction step using the `agg.bg_subtract(...)` function, and (*iii*) adding a bilateral denoising step. This results in the following segmentations.

![otsu_rb](docs/otsu_rb.png)

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