BrainX Ecosystem

braincell.io module

Contents

`braincell.io` module#

braincell.io reads neuronal morphologies from the common file formats and integrates with NeuroMorpho.Org. See File Formats & IO for the task-oriented guide.

SWC#

`SwcReader`
`SwcReadOptions`
`SwcReport`
`SwcIssue`

Neurolucida ASC#

`AscReader`
`AscReport`
`AscIssue`
`AscMetadata`
`AscSpineRecord`

NeuroML2#

NeuroMlReader

NeuroMorpho.Org client#

`load_neuromorpho`	Fetch a NeuroMorpho.Org neuron and return it as a `Morphology`.
`fetch_neuromorpho`	Download files for a NeuroMorpho.Org neuron without parsing.

`NeuroMorphoClient`	Stateful client for the NeuroMorpho.Org REST API.
`NeuroMorphoQuery`	Typed builder for NeuroMorpho.Org search queries.
`NeuroMorphoNeuron`	A single NeuroMorpho.Org neuron record.
`NeuroMorphoMeasurement`	Typed view over a NeuroMorpho.Org morphometry record.
`NeuroMorphoDetail`	Aggregate description of a neuron, including measurement and URLs.
`NeuroMorphoFilePlan`	A planned file download for a single neuron.
`NeuroMorphoDownloadItem`	Result of a single file download for a neuron.
`NeuroMorphoDownloadRecord`	Result of a multi-file download for a neuron.
`NeuroMorphoUrls`	Bundle of URLs related to a single neuron.
`NeuroMorphoSearchPage`	One page of search results from `/api/neuron/select`.
`NeuroMorphoCache`	First-class cache over locally-downloaded NeuroMorpho.Org neurons.
`NeuroMorphoCacheLayout`	Pure path builder for the on-disk NeuroMorpho.Org cache layout.
`NeuroMorphoCacheStatus`	Snapshot of what is cached on disk for a single neuron.

Errors#

`NeuroMorphoError`	Base class for every error raised by the NeuroMorpho.Org client.
`NeuroMorphoHTTPError`	Raised when an HTTP request to NeuroMorpho.Org fails permanently.
`NeuroMorphoNotFoundError`	Raised when a NeuroMorpho.Org resource (typically a neuron id) does not exist.
`CheckpointError`	Raised when a braincell checkpoint cannot be parsed or validated.
`CheckpointVersionError`	Raised when a checkpoint's schema version is not supported by this build.

Checkpointing#

`save_morpho`	Write a `Morpho` to a braincell checkpoint file.
`load_morpho`	Load a `Morpho` from a braincell checkpoint file.
`save_branch`	Write a `Branch` to a braincell checkpoint file.
`load_branch`	Load a `Branch` from a braincell checkpoint file.