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Add additional explanation regarding zero as a label #270

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Dec 11, 2023
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Add additional explanation regarding zero as a label #270

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Add additional explanation regarding zero as a label
stefanhahmann Sep 27, 2023
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Merge branch 'main' into extend_readme_zero_labels
Cryaaa Dec 11, 2023
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11 changes: 6 additions & 5 deletions README.md
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Expand Up @@ -38,8 +38,9 @@ Jump to:

### Starting point
For clustering objects according to their properties, the starting point is a [grey-value image](example_data/blobs.tif) and a label image
representing a segmentation of objects. For segmenting objects, you can for example use the
[Voronoi-Otsu-labelling approach](https://github.com/haesleinhuepf/napari-segment-blobs-and-things-with-membranes#voronoi-otsu-labelling)
representing a segmentation of objects.
The label image should not contain objects with the label `0` as these objects cannot be separated from the background, which is `0` as well in many images and would lead into erroneous behaviour when performing the clustering.
For segmenting objects, you can for example use the [Voronoi-Otsu-labelling approach](https://github.com/haesleinhuepf/napari-segment-blobs-and-things-with-membranes#voronoi-otsu-labelling)
in the napari plugin [napari-segment-blobs-and-things-with-membranes](https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes).

![](https://github.com/BiAPoL/napari-clusters-plotter/raw/main/images/starting_point.png)
Expand All @@ -53,9 +54,9 @@ Select the image, the corresponding label image and the measurements to analyse
A table with the measurements will open and afterwards, you can save and/or close the measurement table.
At this point it is recommended to close the table and the Measure widget to free space for following steps.

You can also load your own measurements you can do this using the menu `Tools > Measurement tables > Load from CSV (nsr)`.
If you load custom measurements, please make sure that there is a `label` column that specifies the which measurement belongs to which labeled object.
Tables for time-lapse data need to include an additional column named `frame`.
You can also load your own measurements. You can do this using the menu `Tools > Measurement tables > Load from CSV (nsr)`.
If you load custom measurements, please make sure that there is a `label` column that specifies which measurement belongs to which labeled object.
Make sure to avoid the label `0` as this is reserved for the background. Tables for time-lapse data need to include an additional column named `frame`.

### Plotting

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