diff --git a/docs/changes.rst b/docs/changes.rst index 50ea56e..789869a 100644 --- a/docs/changes.rst +++ b/docs/changes.rst @@ -6,7 +6,7 @@ Version 0.5.0 * Speed up embedding using Masks * The command ``tomotwin_embed.py tomogram`` now has an optional ``--mask`` argument to select the region of interest for embedding. - * The command ``tomotwin_tools.py embedding_mask`` now computes a by isonet inspired mask that hides some parts of the tomogram volume that are unlikely to contain proteins. If you use the generated mask when running ``tomotwin_embed.py tomogram``, the embedding step is up to 2 times faster. **CAUTION:** In TomoTwin 0.4, the ``embeddings_mask`` command calculated a label mask for the clustering workflow. This functionality now happens automatically during the calculation of the umap (``tomotwin_tools.py umap``). + * The command ``tomotwin_tools.py embedding_mask`` now computes a by isonet inspired mask that hides some parts of the tomogram volume that are unlikely to contain proteins. If you use the generated mask with new ``--mask`` argument, the embedding step is up to 2 times faster. **CAUTION:** In TomoTwin 0.4, the ``embeddings_mask`` command calculated a label mask for the clustering workflow. This functionality now happens automatically during the calculation of the umap (``tomotwin_tools.py umap``). * Thanks Caitie McCafferty and Ricardo Righetto for the feature request * More accurate cluster centers * When selecting clusters in Napari during the clustering workflow, the `Medoid `_ is now calculated instead of the average of all cluster embeddings. This has the advantage that it is guaranteed to be on the embedding hypersphere and should be a better representation of the cluster center than the average.