lopollar

When segmenting nuclei, I often end up with similar issues, where one or two pixels end up outside of the shape. However, when performing segmentation on whole cells, I often...

It is 2D segmentation using the cyto option. The problem arises for me when creating shapes (with shapely) out of the masks after the segmentation. However, when plotting the masks,...

Hi, For me, the first feels like how I wouldcode it myself, so I would prefer that one! Thank you for taking my suggestion into account!

Thank you for this issue, had the same problem and not using pygeos solved the problem, amazing.

Thanks a lot for the code, I did have to adapt one line to make it work for me: ``` #boundaries = gpd.GeoDataFrame(index=[key], geometry=MultiPolygon([Polygon(f['featuredata'][key]['zIndex_3']['p_0']['coordinates'][()][0])])) boundaries = gpd.GeoDataFrame(geometry=gpd.GeoSeries(MultiPolygon([Polygon(f['featuredata'][key]['zIndex_3']['p_0']['coordinates'][()][0])]),index=[key])) ```

Hi, I would also be really interested in this feature. Is there a workaround now that we can draw the shapes in napari and load them up somewhere else?

Hi, I think you have a transformation implementation for MERFISH anyway, right? I would give them both option, a transformation file as input, or a pixel size. Very easy to...

On my own dataset I would suggest following setup: ### Reading in data and annotating shapes - load in dataset (without table, but segmented). I do have it as a...