Post processing

In its current form, MoMA is primarily designed to find the correct lineage in a dataset and does not attempt to get accurate estimates of the sizes and total fluorescence of the cells at each time point. To obtain better estimates of the size and fluorescence of each cell at each time point we developed a post-processing algorithm that, on the datasets that we have tested, can produce accurate estimates of cell size and total fluorescence from the raw output of MoMA. The post-processing code has been implemented as a perl script that we distribute here.

Download moma_refine_size_and_fluo.pl.

Prerequisites

• An installation of perl on your computer.

How to post-process MoMA's results

• Export the results of one growth lane and make sure to includin the pixels intensities (you have to check the corresponding box in the "Data export setup" dialog).
• run perl path/to/moma_refine_size_and_fluo.pl path/to/ExportedResults_basename.csv

This will produce a text file named ExportedResults_basename.refined with the following format:

• one line starting with >CELL … for each cell, giving the following variables:
  • cell_ID: unique identifier of the cell
  • parent_ID: cell_ID of the parent cell
  • daughter-type: the position of the cell at division (BOTTOM or TOP)
  • first-frame: the index of the frame at which the cell was born
  • last-frame: the index of the frame at which the cell has divided
  • type_of_end: the event causing the cell's time series to terminate (div, exit, or eod for end of data)
  • genealogy: a unique identifier representing the cell's genealogy
• this initial line is followed by a series of lines (one per frame) with the following variables:
  • frame
  • vertical_top: vertical pixel coordinate of the top of the box containing the cell
  • vertical_botom: vertical pixel coordinate of the bottom of the box containing the cell
  • cell_num_in_lane: Number of the cell in the growth channel (counting from the open top, i.e the top cell is number 1)
  • total_cell_in_lane: total number of cells in the growth channel at this frame.
  • length: estimated cell length (in pixels)
  • fluo_background: estimated fluorescence intensity of the background
  • fluo_amplitude: estimated total fluorescence coming from the the cell

Here is an excerpt from the top of such a file:

#CELL cell_ID    parent_ID      daughter-type   first-frame     last-frame      type_of_end     genealogy
#frame  vertical_top    vertical_botom  cell_num_in_lane        total_cell_in_lane      length(pixel)   fluo_background fluo_amplitude
>CELL 0 -1      CELL#1  0       16      div     0:1
0       276     313     7       7       31.1    37691.7968922591        1366015.04953921
1       275     313     7       7       32.1    38501.9583209432        1440103.81472803
2       275     313     7       7       33.1    38375.0125242731        1485401.28896109
3       274     313     7       7       33.1    39367.9123372995        1519074.078158
4       273     313     7       7       33.1    40384.3803342231        1547265.45779833
5       273     313     6       6       34.1    39461.0257582768        1595982.85459217
6       272     312     6       6       33.1    39357.9701382282        1630759.17450499
7       272     313     6       6       35.1    40214.1988288816        1651569.96168615
8       271     313     6       6       36.1    41380.1040326225        1680529.9555218
9       269     312     7       7       35.1    43774.6724729415        1700556.07047628