From 1767b80411db1be3ec1d1455ac09f463a12ec2f4 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Wed, 13 Dec 2023 17:12:18 +0100 Subject: [PATCH 1/3] install specific napari clusters plotter --- conda_env_napari.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conda_env_napari.yml b/conda_env_napari.yml index fbde5d5..c898c4f 100644 --- a/conda_env_napari.yml +++ b/conda_env_napari.yml @@ -9,5 +9,6 @@ dependencies: - pip - pip: - napari-boxmanager - - napari-tomotwin + - napari-tomotwin>=0.3.0 + - napari-clusters-plotter@git+https://github.com/BiAPoL/napari-clusters-plotter.git@095d9e8 From a3892bc6f5afad2f74fcef347c19774fe42d9e33 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Thu, 14 Dec 2023 08:29:27 +0100 Subject: [PATCH 2/3] remove loading label_mask from tutorial --- docs/strategies/strategy_01.rst | 2 +- docs/strategies/strategy_03.rst | 2 +- docs/tutorials/tut02_cluster.rst | 6 ++---- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/docs/strategies/strategy_01.rst b/docs/strategies/strategy_01.rst index 9cbbf78..ec72f7d 100644 --- 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 index 334f78a..ab8c83b 100644 --- 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 index 8d05b76..f35a28e 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -23,8 +23,6 @@ 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 ^^^^^^^^^^^^^^^^^^^^^^^^ @@ -32,10 +30,10 @@ Now that we have all the input files for the clustering workflow we can get star .. 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 ^^^^^^^^^^^^^^^^^^^^^^^^ From 49702813f516417ba54c7c129e009aa50ef65e8b Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Thu, 14 Dec 2023 14:17:02 +0100 Subject: [PATCH 3/3] make sure that correct clusters plotter version gets installed --- conda_env_napari.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda_env_napari.yml b/conda_env_napari.yml index c898c4f..4bc2142 100644 --- a/conda_env_napari.yml +++ b/conda_env_napari.yml @@ -9,6 +9,6 @@ dependencies: - pip - pip: - napari-boxmanager - - napari-tomotwin>=0.3.0 + - napari-tomotwin - napari-clusters-plotter@git+https://github.com/BiAPoL/napari-clusters-plotter.git@095d9e8