## lamindb.integrations

Integrations.

# Functions

lamindb.integrations.save_vitessce_config(vitessce_config, key=None, description=None)

 Validates and saves a "VitessceConfig" object.

 If the "VitessceConfig" object references multiple artifacts,
 automatically creates a "Collection" and displays the "Vitessce
 button" next to it.

 The "VitessceConfig" artifact has ".suffix = ".vitessce.json"" and
 ".kind = "__lamindb_config__"", which is by default hidden on the
 hub UI.

 Guide: Vitessce: AnnData.

 Parameters:
 * **vitessce_config** ("VitessceConfig") -- A "VitessceConfig"
 object.

| * **key** ("str" | "None", default: "None") -- A "key" for the |
 "VitessceConfig" artifact.

| * **description** ("str" | "None", default: "None") -- A |
 "description" for the "VitessceConfig" aritifact. Is
 additionally used as "key" for a "Collection" in case the
 "VitessceConfig" object references multiple artifacts.

 Return type:
 "Artifact"

lamindb.integrations.save_tiledbsoma_experiment(adatas, key=None, description=None, run=None, revises=None, measurement_name='RNA', obs_id_name='obs_id', var_id_name='var_id', append_obsm_varm=False, **kwargs)

 Write "AnnData" to "tiledbsoma.Experiment".

 Reads "AnnData" objects, writes them to "tiledbsoma.Experiment",
 creates & saves an "Artifact".

 Populates a column "lamin_run_uid" column in "obs" with the current
 "run.uid".

 Is based on tiledbsoma.io.from_anndata.

 Parameters:
| * **adatas** (list[AnnData | UPathStr]) -- "AnnData" objects to |
 write, in-memory or on-disk.

| * **key** (str | None, default: "None") -- An optional key to |
 reference the artifact.

| * **description** (str | None, default: "None") -- A |
 description.

| * **run** (Run | None, default: "None") -- The run that creates |
 the artifact.

| * **revises** (Artifact | None, default: "None") -- |
 "lamindb.Artifact" with "tiledbsoma.Experiment" to append to.

 * **measurement_name** (str, default: "'RNA'") -- The name of
 the measurement to store data in "tiledbsoma.Experiment".

 * **obs_id_name** (str, default: "'obs_id'") -- Which "AnnData"
 "obs" column to use for append mode.

 * **var_id_name** (str, default: "'var_id'") -- Which "AnnData"
 "var" column to use for append mode.

 * **append_obsm_varm** (bool, default: "False") -- Whether to
 append "obsm" and "varm" in append mode .

 * ****kwargs** -- Keyword arguments passed to
 "tiledbsoma.io.from_anndata".

 Return type:
 Artifact

lamindb.integrations.curate_from_croissant(croissant_data, run=None)

 Create annotated artifacts from a CroissantML file.

 Returns a collection if multiple files are found in
 "croissant_data", otherwise a single artifact.

 Parameters:
| **croissant_data** ("str" | "Path" | "dict"["str", "Any"]) -- |
 Path to CroissantML JSON file or dictionary.

 Return type:
| "Artifact" | "Collection" |

 -[ Example ]-

 artifact = ln.integrations.curate_from_croissant("dataset_metadata.json")

# Modules

| --- | --- |
| "lightnin | PyTorch Lightning integration for LaminDB. |
| g" |
| --- | --- |

* lamindb.integrations.lightning

  * "Checkpoint"

 * "Checkpoint.setup()"

  * "SaveConfigCallback"

 * "SaveConfigCallback.setup()"

  * "save_lightning_features()"