ParseBrownian and BrownianXMLtoTIFF are two scripts written in Python that allow the user to convert the output from the brownianMotion simulator to Microscope Simulator formatted XML files (ParseBrownian) to TIFF files of each Z-stack (BrownianXMLtoTIFF). ParseBrownian allows the user to specify which points from the brownianMotion simulator are fluorescing based on a colors file generated by the brownianMotion application, allowing scientists to generate fluorescence microscope videos of simulations supposing that specific structures in the simulation are fluorescently labeled.
Author: Joseph K. Aicher
Plugin originally written as part of a summer project with Professor Russell M. Taylor II for the UNC CAP REU and CISMM during the summer of 2013.
Note: this file is written in Markdown for easy formatting into HTML.
These scripts require you to have Python installed. ParseBrownian and BrownianXMLtoTIFF were written using Python 3.3.2; however, they should work with any version of Python above 2.6.
BrownianXMLtoTIFF requires you to have Microscope Simulator installed from the CISMM website.
As Python scripts, ParseBrownian and BrownianXMLtoTIFF do
not need to be installed. However, ParseBrownian must be
kept in the same folder as colored_spheres_list.py and micro_sphere.py.
We will assume that the locations of ParseBrownian
and BrownianXMLtoTIFF are $ParseBrownian and $BrownianXMLtoTIFF.
ParseBrownian allows you to convert the output of the brownianMotion simulator to XML files readable by Microscope Simulator. Recall that from the brownianMotion simulator you get two files: one with the coordinates at each time and one with the "color" of each coordinate, where the "color" is some integer value. Using these files, along with optional arguments that you can specify, ParseBrownian will generate an XML file for Microscope Simulator at each point in time for coordinates matching specific colors, setting their color channel to green.
We will assume that the locations of the coordinates file and
the colors file are $coordinates and $point_colors.
Running ParseBrownian, at its simplest, boils down to the following command:
> python $ParseBrownian $point_colors $coordinates
Running that command will automatically create a Microscope
Simulator file using color 4 for each time step to a directory
titled "output," along with other settings that were specific
to the script's original use case. These parameters can be changed
by adding commandline arguments before $point_colors, so that
the command being run would be:
> python $ParseBrownian [args] $point_colors $coordinates
where [args] specify parameters of interest. A useful example
of this would be:
> python $ParseBrownian -random 1 1 1 -zxy -use_colors colors.txt -PSF PSF_gain.txt -out myoutput -width 300 -height 300 -noise 3.5 -every 10 $point_colors $coordinates
This will translate the coordinates found in $coordinates by a
random vector +/- 1 micron in the three coordinate directions,
rotate the coordinate system so that the simulation z-axis is parallel
to the focal planes, set the colors and PSF/gain values being used
to those found in colors.txt and PSF_gain.txt in the current
directory, set the output directory to "myoutput," set the width and height
of the output microscope images would to 300 pixels, add simulated
Gaussian noise with a standard deviation of 3.5, and only use every
10th time step.
The -PSF flag deserves extra mention. You must specify a point
spread function that you have put into Microscope Simulator. The
details of adding a point spread function to Microscope Simulator
are beyond the scope of this README. Assuming that you have a point
spread function named "GFP" in Microscope Simulator and would
like to simulate it with a gain of 15, you could make a file named
GFPgain15.txt with "GFP" as the first line and "15" as the second
line. You will probably need to adjust the gain before moving on to
BrownianXMLtoTIFF to ensure that you get an image.
More information about the commandline flags can be found by running the command:
> python $ParseBrownian -help
BrownianXMLtoTIFF allows you to convert the output of ParseBrownian
to TIFF files of the microscope stack at each time step. Recall that
the output of ParseBrownian is put into some folder. We will assume
that the path to that folder is $input_folder.
Running BrownianXMLtoTIFF, at its simplest, boils down to the following command:
> python $BrownianXMLtoTIFF $input_folder
Running that command will automatically create TIFF files for
each XML file in $input_folder for the red, green, and blue color
channels and put them into a folder named output_tiff in the
current directory, so long as Microscope Simulator is installed to the path
C:\Program Files (x86)\CISMM\Microscope Simulator 2.3.0\bin\MicroscopeSimulator.exe.
Note that this program takes a while to complete because Microscope
Simulator is a graphics-intensive program, so while it runs you may
want to grab a cup of coffee or go to lunch. Unfortunately, due
to how Microscope Simulator is written, it will take up your first
(and possibly only) computer screen while it runs.
You will typically only care about the green channel. Meanwhile,
you may want to have the TIFF files go to a folder named something
else, say "different". Microscope Simulator may be installed
somewhere else, which we will suppose is $microscope_path. We
can make the script only output the green channel to the folder
different using Microscope Simulator installed to
$microscope_path by using the following command:
> python $BrownianXMLtoTIFF -green -out different -simulator $microscope_path $input_folder
More information about the commandline flags can be found by running the command:
> python $BrownianXMLtoTIFF -help