simi.py

Parse and access cell lineage data from Simi BioCell using Python.

Usage example

First go into Python prompt:

user@computer:~/path/to/simi.py$ python

Python 2.7.13 (default, Jan 19 2017, 14:48:08) 
[GCC 6.3.0 20170118] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 

Now import the simi.py library to load and parse .sbc and .sbd files.

# Load library.
import simi

# Parse .sbc and .sbd files of a SimiProject.
s = simi.SimiProject(sbc_file="lineage.sbc", sbd_file="lineage.sbd")

Access cell lineage data.

# The .sbc file contains all settings of the project.
print s.sbc.settings
{'3DCENTER': {'AUTO': '1',
  'CHECK': '1',
  'CX': '458',
  'CY': '262',
  'DX': '0',
  'DY': '0',
  'LBX': '0',
  ...

# The .sbd file contains all the tracked cells.
print s.sbd.cells
OrderedDict([('ABCD', <simi.Cell instance at 0x7fb27c5803f8>),
             ('CD', <simi.Cell instance at 0x7fb27c5806c8>),
             ('D', <simi.Cell instance at 0x7fb27c5805a8>),
             ('1D', <simi.Cell instance at 0x7fb27c580fc8>),
             ('2D', <simi.Cell instance at 0x7fb27c580368>),
             ('3D', <simi.Cell instance at 0x7fb27c580e18>),
             ('4D', <simi.Cell instance at 0x7fb27c5c6d88>),
             ...

Get information from every individual cell and tracked spots.

# Access each cell individually by name.
c = s.sbd.cells['3D']
print c.parent
CELL=2D

# Get all spots with xyz coordinates:
for spot in c.spots:
    print spot.frame, spot.x, spot.y, spot.z

329 241 34 348
320 256 39 369
324 256 40 381
326 251 42 409
326 248 40 426
322 248 41 430
...

Convert Simi to MaMuT

simi2mamut.py is the script I use to convert my Simi lineage files to MaMuT. It will not work as is on your own lineage files, but it should work after adaptating the code. Please check out the script documentation and let me know if you run into issues.

Disclaimer

The code has only been tested in my own lineage files. I had to manually fix some issues with Simi format before parsing. Most crucial is to make sure each cell has a unique name. The library also cannot handle very well alternative lineages, if present. Always double check the data before analysing!

Please report any issues.

Citation

The code herein is part of the following publication:

Vellutini, B. C., Martín-Durán, J. M. & Hejnol, A. Cleavage modification did not alter blastomere fates during bryozoan evolution. BMC Biol. 15, 33 (2017). doi: 10.1186/s12915-017-0371-9