Package sc.fiji.snt.io

Class MouseLightQuerier

java.lang.Object
sc.fiji.snt.io.MouseLightQuerier
public class MouseLightQuerier extends Object
Importer for retrieving reconstructions from MouseLight's online database at ml-neuronbrowser.janelia.org
Author:
Tiago Ferreira

  • Method Details

    • isDatabaseAvailable

      public static boolean isDatabaseAvailable()
      Checks whether a connection to the MouseLight database can be established.
      Returns:
      true, if an HHTP connection could be established

    • getIDs

      public static List<String> getIDs(AllenCompartment compartment)
      Gets neuron IDs for the specified brain compartment.
      Parameters:
      compartment - the Allen brain compartment
      Returns:
      list of neuron IDs in the compartment

    • getIDs

      public static List<String> getIDs(Collection<AllenCompartment> compartments)
      Gets neuron IDs for the specified collection of brain compartments.
      Parameters:
      compartments - the collection of Allen brain compartments
      Returns:
      list of neuron IDs in the compartments

    • getIDs

      public static List<String> getIDs(String idOrDOI, boolean exactMatch)
      Returns a list of IDs associated with the specified identifier
      Parameters:
      idOrDOI - the neuron id (e.g., "AA0001") or DOI (e.g., "10.25378/janelia.5527672") of the neuron to be loaded
      exactMatch - If true, only exact matches will be considered

    • getIDs

      public static List<String> getIDs(Collection<String> idsOrDOIs, boolean exactMatch)
      Gets neuron IDs matching the specified collection of IDs or DOIs.
      Parameters:
      idsOrDOIs - the collection of IDs or DOIs to search for
      exactMatch - if true, only exact matches will be considered
      Returns:
      list of matching neuron IDs

    • getAllIDs

      public static List<String> getAllIDs()
      Gets all available neuron IDs from the database.
      Returns:
      list of all neuron IDs

    • setCCFVersion

      public static void setCCFVersion(String version)
      Sets the version of the Common Coordinate Framework to be used by the Querier.
      Parameters:
      version - Either "3" (the default), or "2.5" (MouseLight legacy)

    • getNeuronCount

      public static int getNeuronCount()
      Gets the number of cells publicly available in the MouseLight database.
      Returns:
      the number of available cells, or -1 if the database could not be reached.

    • main

      public static void main(String... args)