Example for CellH5’s relational data representation in HDF5
Event Object
Tracking
obj_idx1
obj_id obj_idx1 obj_idx2
0
0
42
0
42
85
…
1
1
43
1
43
86
…
2
3
45
2
45
88
Nucleus to Cell
obj_idx_1
obj_idx_2
0
1
…
42
43
44
45
…
1
Nucleus
time_idx obj_label_idx
0
7
0
8
…
42
1
4
43
1
6
…
85
2
2
86
2
3
…
0
1
3
0
1
42
43
44
45
2
time_idx obj_label_idx
0
0
0
1
…
42
1
0
43
1
1
…
85
2
0
86
2
1
…
Center
x
Cell
0
1
obj_idx2
0
42
42
85
…
140
353
134
347
135
348
136
349
…
4
object
object feature
object relation
region object
y
0
1
119
719
33
16
42
43
796
215
35
20
85
86
936
…
55
Object Feature
area
intensity
0
1
119
719
33
16
42
43
796
215
35
20
85
86
936
55
…
1
A (temporal) object from Event object with obj_id 0 connects two nucleus
region objects with indices 0 and 42.
2
The nucleus indices are used to look up the time and and segmentation label indices
in the Nucleus dataset and the center positions in the Center object feature dataset.
3
The indices of the nuclei objects are related to the Cell indices with the
Nucleus to Cell object relation (in this case one-to-one relation).
4
The cell object indices are used to look up the time and segmenation label
indices from the Cell region object. Area and intensity are retrived from
Image Feature object feature dataset.