diff --git a/docs/changes.rst b/docs/changes.rst index a9ff962..789869a 100644 --- a/docs/changes.rst +++ b/docs/changes.rst @@ -1,13 +1,19 @@ Changes ======= -Version 0.5.0 (upcoming) +Version 0.5.0 ************* -* The ``tomotwin_embed.py tomogram`` command has now a optional ``--mask`` option to select region of interestes for embeddings. -* The ``tomotwin_tools.py embedding_mask`` now calculates a mask that masks out some portions of the tomogram volume that probably do not contain proteins. Using the generated mask when running ``tomotwin_embed.py tomogram``, the embeddings step is 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``). -* For the clustering workflow, you can now calculate the medoid instead of arithmetic mean. This should be a much better representation of the cluster center. - +* 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 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. + * The coordinates of the found medoid for each cluster is written as a .coords file to disk. +* Other + * Updated installation instructions for napari: Napari 0.4.17 -> Napari 0.4.18 + * :ref:`Added some information snippets for developers ` Version 0.4.3 ************* diff --git a/docs/developer/devs.rst b/docs/developer/devs.rst index 5d9bea6..a16b8e1 100644 --- a/docs/developer/devs.rst +++ b/docs/developer/devs.rst @@ -1,3 +1,4 @@ +.. _dev-info: Developer information ===================== diff --git a/docs/installation.rst b/docs/installation.rst index 610ab15..0adcd22 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -24,7 +24,7 @@ Here we assume that you don't have napari installed. Please do: .. prompt:: bash $ - mamba create -y -n napari-tomotwin -c conda-forge python=3.10 napari=0.4.17 pyqt pip + mamba create -y -n napari-tomotwin -c conda-forge python=3.10 napari=0.4.18 pyqt pip conda activate napari-tomotwin Install the required plugins `napari-boxmanager` and `napari-tomotwin` via pip: