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 |
---|---|
flimage version |
flimage software version used |
identifier |
image identifier |
qpimage version |
qpimage software version used |
sim center |
Simulation: center of object [px] |
sim model |
Simulation: model used |
sim radius |
Simulation: object radius [m] |
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.