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Merge pull request #4 from royerlab/textual-changes-Teun
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JoOkuma authored Oct 24, 2024
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Expand Up @@ -159,7 +159,7 @@ The `Tracker` class is configured with a `MainConfig` object, which contains the
print(MainConfig())
```

The minimum are is an important parameter, otherwise we will have too many hypotheses to track, we can easily find this information from the previous segmentation.
The minimum area is an important parameter, otherwise we will have too many hypotheses to track, we can easily find this information from the previous segmentation.

```{admonition} Interaction
Select a cell and a time point in napari, edit the cell_id and cell_time_point variables below, and run the cell to find the size of the cell.
Expand Down Expand Up @@ -236,7 +236,7 @@ While this approach provides a good starting point and highlights how classical
## Cellpose segmentation

First, we define a function to predict the segmentation using Cellpose and the `cyto2` model.
The `diamond` parameter is set to 75.0, which is a good starting point for this dataset.
The `diameter` parameter is set to 75.0, which is a good starting point for this dataset.
We also disable the normalization step in Cellpose, as we are doing our own normalization using the `gamma` parameter for contrast adjustment.

```{code-cell} ipython3
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