Merge pull request #84 from MPI-Dortmund/release_08

Release v0.8.0
MPI-Dortmund · Dec 14, 2023 · 66dbd48 · 66dbd48
2 parents ee801ff + 4970281
commit 66dbd48
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diff --git a/conda_env_napari.yml b/conda_env_napari.yml
@@ -10,4 +10,5 @@ dependencies:
   - pip:
       - napari-boxmanager
       - napari-tomotwin
+      - napari-clusters-plotter@git+https://github.com/BiAPoL/napari-clusters-plotter.git@095d9e8
 
diff --git a/docs/strategies/strategy_01.rst b/docs/strategies/strategy_01.rst
@@ -48,7 +48,7 @@ To start napari run:
 
  .. prompt:: bash $
 
-    napari tomo/tomo.mrc umap/tomo_embeddings_filtered_allrefs_label_mask.mrci
+    napari tomo/tomo.mrc
 
 After starting napari, load the clustering plugin: :guilabel:`Plugins` -> :guilabel:`napari-tomotwin` -> :guilabel:`Cluster umap embeddings`.
 

diff --git a/docs/strategies/strategy_03.rst b/docs/strategies/strategy_03.rst
@@ -67,7 +67,7 @@ To start napari run:
 
  .. prompt:: bash $
 
-    napari tomo/tomo.mrc umap/tomo_embeddings_filtered_label_mask.mrci
+    napari tomo/tomo.mrc
 
 After starting napari, load the clustering plugin: :guilabel:`Plugins` -> :guilabel:`napari-tomotwin` -> :guilabel:`Cluster umap embeddings`.
 

diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst
@@ -23,19 +23,17 @@ Now we will approximate the tomogram embeddings to 2D to allow for efficient vis
     If you encounter an out of memory error here, you may need to reduce the :guilabel:`fit_sample_size` and/or :guilabel:`chunk_size` values (default 400,000).
 
 
-Additionally, it generated a mask (`tomo_embeddings_label_mask.mrci`) of the embeddings to allow us to track which UMAP values correspond to which points in the tomogram.
-
 4. Load data for clustering in Napari
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 Now that we have all the input files for the clustering workflow we can get started in Napari. First open your tomogram and the embedding mask by:
 
 .. prompt:: bash $
 
-    napari your_tomo_a10.mrc out/clustering/your_tomo_a10_embedding_label_mask.mrci
+    napari your_tomo_a10.mrc
 
 Next open the napari-tomotwin clustering tool via :guilabel:`Plugins` -> :guilabel:`napari-tomotwin` -> :guilabel:`Cluster UMAP embeddings`. Then choose the :guilabel:`Path to UMAP` by clicking on :guilabel:`Select file` and provide the path to your :file:`your_tomo_a10_embeddings.tumap`. 
-Click :guilabel:`Load` and after a second, a 2D plot of the umap embeddings should appear in the plugin window.
+Click :guilabel:`Load` and a 2D plot of the umap embeddings should appear in the plugin window.
 
 5. Find target clusters
 ^^^^^^^^^^^^^^^^^^^^^^^^