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.


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

graph example {
    graph [rankdir=LR];
    FLImage [shape="folder", label="/"];
    fluorescence [shape="folder"];
    raw [shape="component"];
    bg_data [shape="folder"];
    data [shape="component"];
    FLImage -- fluorescence;
    fluorescence -- raw;
    fluorescence -- bg_data;
    bg_data -- data;


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



pixel size

detector pixel size [m]


acquisition time of the image [s]

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



flimage version

flimage software version used


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]


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.


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

graph example {
    node [shape="folder"];
    graph [rankdir=LR, center=1];
    FLSeries [label="/"]
    fl1 [label="fli_0"]
    fl2 [label="fli_1"]
    a1 [shape="box", label=fluorescence];
    d0 [shape="box", label="..."];
    d2 [shape="box", label="..."];
    d3 [shape="box", label="..."];
    d4 [shape="box", label="..."];
    fl3 [label="fli_47"]
    FLSeries -- fl1;
    fl1 -- a1;
    a1 -- d0;
    FLSeries -- fl2;
    fl2 -- d2;
    FLSeries -- d4;
    FLSeries -- fl3;
    fl3 -- d3;

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.