File Format¶
Base file format¶
Currently Cockpoit 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 exended header to store specific optical microscopy meta-data. 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 are all set to zero.
Followed by 32 32bit floats. We only what the first 14 are:
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 realtively uncommon format, the .dv file format is supprted by the bioformats project allowing import of .dv files into software using this library 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 microscopes utilising the commerical package SoftWoRx.