File Format¶
Base file format¶
Currently Cockpit only supports the dv file format which is an extension of the mrc file format. The mrc file format is defined in detail in MRC/CCP4 2014 file format specification. The CCP4 consortium of the EM community are continuing to support and extend this file format. This support includes file validators and a detailed specification, which is compatible with the files used here but not identical.
Cockpit utilises the extended header to store specific optical microscopy metadata. In particular both the excitation and emission wavelengths must be set to correctly select the SIM fitting bootstrap parameters including stripe width and k0 angles.
DV file header specification¶
The extended header has the following structure per plane (see Cockpit github issue #290):
8 32bit signed integers, often all set to zero.
Followed by 32 32bit floats. We only know what the first 14 mean:
Float index |
Meta data content |
|---|---|
0 |
photosensor reading (typically in mV) |
1 |
elapsed time (seconds since experiment began) |
2 |
x stage coordinates |
3 |
y stage coordinates |
4 |
z stage coordinates |
5 |
minimum intensity |
6 |
maximum intensity |
7 |
mean intensity |
8 |
exposure time (seconds) |
9 |
neutral density (fraction of 1 or percentage) |
10 |
excitation wavelength |
11 |
emission wavelength |
12 |
intensity scaling (usually 1) |
13 |
energy conversion factor (usually 1) |
Software supporting dv files¶
Although a relatively uncommon format, the dv file format is well supported by Bioformats and so supported by most bioimaging programs, including ImageJ, OMERO and Matlab. Additionally, the Chromagnon image alignment tool will read and write dv files and it is the native format for DeltaVision and OMX microscopes utilising the commercial package SoftWoRx.