.. _api: API Reference ============= .. _api_fetch: Connecting to a Server ++++++++++++++++++++++ Connections to servers are represented by a ``CatmaidInstance`` object. You can either initialize it directly or store credentials as environmental variables and use :func:`~pymaid.connect_catmaid` to do that for you. .. autosummary:: :toctree: generated/ pymaid.connect_catmaid pymaid.CatmaidInstance pymaid.CatmaidInstance.copy pymaid.CatmaidInstance.clear_cache pymaid.CatmaidInstance.fetch pymaid.CatmaidInstance.load_cache pymaid.CatmaidInstance.make_url pymaid.CatmaidInstance.setup_cache pymaid.CatmaidInstance.save_cache Fetching data +++++++++++++ This section contains functions to pull data from a CATMAID server. Neurons ------- Functions related to searching for neurons and fetching their 3D skeletons: .. autosummary:: :toctree: generated/ pymaid.find_neurons pymaid.get_arbor pymaid.get_names pymaid.get_neuron pymaid.get_neuron_id pymaid.get_neurons_in_volume pymaid.get_origin pymaid.get_skids_by_annotation pymaid.get_skids_by_name pymaid.get_skids_by_origin pymaid.get_skeleton_change pymaid.get_skeleton_ids Neuron labels ^^^^^^^^^^^^^ .. autosummary:: :toctree: generated/ pymaid.neuron_label.NeuronLabeller pymaid.neuron_label.SkeletonId pymaid.neuron_label.NeuronName pymaid.neuron_label.Annotations pymaid.neuron_label.ThinNeuron Annotations ----------- Functions to fetch annotations: .. autosummary:: :toctree: generated/ pymaid.get_annotated pymaid.get_annotations pymaid.get_annotation_details pymaid.get_user_annotations pymaid.get_annotation_id pymaid.get_entity_graph Nodes ----- Functions to fetch nodes and connectors: .. autosummary:: :toctree: generated/ pymaid.find_nodes pymaid.get_connectors_in_bbox pymaid.get_skid_from_node pymaid.get_node_details pymaid.get_nodes_in_volume pymaid.get_node_location pymaid.get_node_table pymaid.get_node_info Tags ---- Functions to fetch node tags: .. autosummary:: :toctree: generated/ pymaid.get_label_list pymaid.get_node_tags Connectivity ------------ Functions to fetch connectivity data: .. autosummary:: :toctree: generated/ pymaid.adjacency_matrix pymaid.adjacency_from_connectors pymaid.cn_table_from_connectors pymaid.get_connectivity_counts pymaid.get_connectors pymaid.get_connector_details pymaid.get_connectors_between pymaid.get_connector_links pymaid.get_connectors_in_bbox pymaid.get_edges pymaid.get_partners pymaid.get_partners_in_volume pymaid.get_nth_partners pymaid.get_paths .. _api_userstats: User stats ---------- Functions to fetch user stats: .. autosummary:: :toctree: generated/ pymaid.get_contributor_statistics pymaid.get_history pymaid.get_logs pymaid.get_transactions pymaid.get_team_contributions pymaid.get_time_invested pymaid.get_user_list pymaid.get_user_contributions pymaid.get_user_stats Volumes ------- Functions to fetch volumes (meshes): .. autosummary:: :toctree: generated/ pymaid.get_volume Landmarks --------- Functions to fetch data about landmarks. .. autosummary:: :toctree: generated/ pymaid.get_landmarks pymaid.get_landmark_groups pymaid.LandmarkMatcher pymaid.CrossProjectLandmarkMatcher Reconstruction samplers ----------------------- Functions for reconstruction samplers: .. autosummary:: :toctree: generated/ pymaid.get_sampler pymaid.get_sampler_domains pymaid.get_sampler_counts Image metadata -------------- Functions to fetch information about the image stacks CATMAID knows about. .. autosummary:: :toctree: generated/ pymaid.get_stacks pymaid.get_stack_info pymaid.get_mirror_info Image data (tiles and N5 volumes) ------------------ Functions to fetch and process image data. Note that this is not imported at top level but has to be imported explicitly:: >>> from pymaid import tiles >>> help(tiles.crop_neuron) >>> from pymaid.stack import Stack >>> help(Stack) .. autosummary:: :toctree: generated/ pymaid.tiles.TileLoader pymaid.tiles.crop_neuron pymaid.stack.Stack .. _api_misc: Misc ---- Functions to fetch miscellaneous data: .. autosummary:: :toctree: generated/ pymaid.clear_cache pymaid.has_soma pymaid.get_cable_lengths pymaid.get_import_info pymaid.get_review pymaid.get_review_details pymaid.url_to_coordinates .. _api_upload: Uploading data ++++++++++++++ Functions to push data to a CATMAID server. Use these with caution! Neurons ------- Upload, rename, move or delete neurons: .. autosummary:: :toctree: generated/ pymaid.delete_neuron pymaid.differential_upload pymaid.push_new_root pymaid.rename_neurons pymaid.replace_skeleton pymaid.join_skeletons pymaid.transfer_neuron pymaid.update_radii pymaid.upload_neuron Annotations ----------- Edit neuron annotations: .. autosummary:: :toctree: generated/ pymaid.add_annotations pymaid.add_meta_annotations pymaid.remove_annotations pymaid.remove_meta_annotations Nodes ----- Edit nodes: .. autosummary:: :toctree: generated/ pymaid.add_node pymaid.delete_nodes pymaid.join_nodes pymaid.move_nodes pymaid.set_nodes_reviewed pymaid.update_node_confidence Connectivity ------------ Edit connectors and connector links: .. autosummary:: :toctree: generated/ pymaid.add_connector pymaid.link_connector Tags ---- Edit tags: .. autosummary:: :toctree: generated/ pymaid.add_tags pymaid.delete_tags Volumes ------- Upload volumes: .. autosummary:: :toctree: generated/ pymaid.upload_volume .. _api_neurons: CatmaidNeuron/List ++++++++++++++++++ Neuron/List objects representing neurons and lists thereof: .. autosummary:: :toctree: generated/ pymaid.CatmaidNeuron pymaid.CatmaidNeuronList :class:`~pymaid.CatmaidNeuron` are a subclasses of _ ``TreeNeuron`` and as such can be used with ``navis`` functions. CatmaidNeuron/List methods -------------------------- Methods common to both ``CatmaidNeurons`` and ``CatmaidNeuronLists``: .. autosummary:: :toctree: generated/ pymaid.CatmaidNeuron.copy pymaid.CatmaidNeuron.downsample pymaid.CatmaidNeuron.plot3d pymaid.CatmaidNeuron.plot2d pymaid.CatmaidNeuron.prune_by_strahler pymaid.CatmaidNeuron.prune_by_volume pymaid.CatmaidNeuron.prune_distal_to pymaid.CatmaidNeuron.prune_proximal_to pymaid.CatmaidNeuron.prune_by_longest_neurite pymaid.CatmaidNeuron.prune_twigs pymaid.CatmaidNeuron.reroot pymaid.CatmaidNeuron.reload pymaid.CatmaidNeuron.resample pymaid.CatmaidNeuron.summary CatmaidNeuronList-specific -------------------------- Methods specific to CatmaidNeuronLists: .. autosummary:: :toctree: generated/ pymaid.CatmaidNeuronList.to_selection pymaid.CatmaidNeuronList.from_selection pymaid.CatmaidNeuronList.has_annotation pymaid.CatmaidNeuronList.head pymaid.CatmaidNeuronList.tail pymaid.CatmaidNeuronList.itertuples pymaid.CatmaidNeuronList.remove_duplicates pymaid.CatmaidNeuronList.sample pymaid.CatmaidNeuronList.summary pymaid.CatmaidNeuronList.mean pymaid.CatmaidNeuronList.sum pymaid.CatmaidNeuronList.sort_values .. _api_morph: Working with Neurons ++++++++++++++++++++ As said previously, :class:`~pymaid.CatmaidNeuron` can be used with _. This includes functions to manipulate (e.g. prune, subset, resample), analyze (e.g. strahler index, synapse flow) or plot neurons. In addition, ``pymaid`` has a few more CATMAID-specific functions: Morphology ---------- .. autosummary:: :toctree: generated/ pymaid.remove_tagged_branches pymaid.time_machine pymaid.prune_by_length pymaid.union_neurons Analysis -------- Various morphology metrics: .. autosummary:: :toctree: generated/ pymaid.arbor_confidence Predicting connectivity ----------------------- Function to predict connectivity: .. autosummary:: :toctree: generated/ pymaid.predict_connectivity Analyses -------- Functions to analyse connectivity: .. autosummary:: :toctree: generated/ pymaid.cluster_by_connectivity pymaid.cluster_by_synapse_placement pymaid.ClustResults pymaid.connection_density pymaid.sparseness Filtering --------- Functions to filter connectivity data: .. autosummary:: :toctree: generated/ pymaid.filter_connectivity pymaid.shared_partners .. _api_utility: Utility +++++++ Various utility functions. .. autosummary:: :toctree: generated/ pymaid.eval_skids pymaid.set_pbars pymaid.set_loggers pymaid.shorten_name