HDF5 file format

The data of a flimage.FLImage or flimage.FLSeries can be stored on disk, using the h5file parameter upon class instantiation. This section describes the scheme used to store the data using the HDF5 file format.

FLImage

The following graph visualized the HDF5 file structure of an FLImage instance:

Attributes

These attributes of the root group (/) describe physical parameters of the data:

key	description
pixel size	detector pixel size [m]
time	acquisition time of the image [s]

These other attributes may be used by e.g. data simulators such as cellsino:

key	description
angle	tomographic acquisition angle [rad]
date	acquisition date ‘YYYY-MM-DD’
device	imaging device used
flimage version	flimage software version used
focus	focus position [m]
identifier	image identifier
numerical aperture	numerical aperture
pos x	x position [m]
pos y	y position [m]
qpimage version	qpimage software version used
sim center	simulation: center of object [px]
sim model	simulation: model used
sim radius	simulation: object radius [m]
software	imaging software used

Groups

The group fluorescence does not hold attributes. It contains a dataset called raw (the raw fluorescence image) and a group called bg_data which may contain a dataset data, a simple background image.

FLSeries

The following graph visualized the HDF5 file structure of an FLSeries instance (with a total of 48 FLImages):

Note that the name of each FLImage group always starts with “fli_” and that the enumeration does not contain leading zeros. The root node (/) of an FLSeries may have the identifier attribute.