Data structures#
Locan provides LocData
as the one data class to deal with the following data structures:
localization data
selections of localization data
collections of selections
Locan provides LocData
as the one data class to deal with the following data structures:
localization data
selections of localization data
collections of selections
Comments on LocData:#
Localization data consists of a list of individual localizations with spatial coordinates and several other properties (detailed list in Properties) like
There is no fundamental difference between 2D and 3D localization data.
Multiple sets of localization data like two-color localizations will be represented by independent
LocData
objects.The unit for length throughout the project is given by the input unit for localization coordinates, unless specified in the metadata. In most cases the unit will be nanometre.
A
LocData
object is typically instantiated from an experimental or simulated localization dataset. The list of localizations is represented in apandas.DataFrame
under the attributeLocData.data
. In additionLocData
has some single-number-properties describing the dataset as a whole. Such properties could be (detailed list in Properties):A
LocData
object can also be instantiated from a selection of localizations. Selections carry a reference to anotherLocData
object and a list of selected indices to not copy the original dataset with all localization properties for each selection. This way a large set of selections can be created with minimal memory requirements.A
LocData
object can also represent a list of selections as e.g. generated by clustering the localization data. TheLocData.data
of a collection consists of the list of all properties from the collectedLocData
(e.g. selections).For the spatial coordinates in each
LocData
object there are various hulls that might be of interest:minimal bounding box
convex hull
alpha complex or alpha shape
minimal oriented bounding box
These hulls are provided from stand-alone methods or through
LocData
attributes. Hull objects expose attributes such asLocData.region_measure
(among others) that are also added asLocData
properties.Other
LocData
properties might be provided by independent methods.