MoMA Properties Old - nimwegenLab/moma GitHub Wiki

• MoMA-Properties-New

MoMA exposes some parameters to the user in two properties files. One contains default parameters for all available parameters and will be loaded every time MoMA is started, the other can optionally be used via a command line parameter and only needs to contain those properties that should diverge from the values set in the global properties file.

The global properties file

When MoMA starts it will look for a file called 'mm.properties' i) in the current folder, and ii) anywhere in the Java Classpath. In case such a file is not found, MoMA will use default values for all parameters (see below) and create such a file at termination time. The following message printed on the console will indicate this:

No default properties file 'mm.properties' found in current path or classpath... I will create one at termination time!

Example properties file (showing default parameter values):

#MotherMachine properties
#Sun Sep 18 16:02:24 EDT 2016
GL_OFFSET_BOTTOM=-1
GUROBI_TIME_LIMIT=15.0
SIGMA_PRE_SEGMENTATION_Y=0.0
SIGMA_PRE_SEGMENTATION_X=0.0
MIN_GAP_CONTRAST=0.019999999552965164
BGREM_TEMPLATE_XMIN=20
DEFAULT_PATH=/Users/julou
BGREM_TEMPLATE_XMAX=35
GUI_WIDTH=640
GL_FLUORESCENCE_COLLECTION_WIDTH_IN_PIXELS=100
GUROBI_MAX_OPTIMALITY_GAP=0.99
BGREM_X_OFFSET=35
GUI_HEIGHT=783
GUI_CONSOLE_WIDTH=600
MIN_CELL_LENGTH=18
GL_OFFSET_LATERAL=20
GUI_POS_Y=100
GUI_POS_X=100
MOTHER_CELL_BOTTOM_TRICK_MAX_PIXELS=10
SIGMA_GL_DETECTION_Y=0.0
GL_OFFSET_TOP=50
SIGMA_GL_DETECTION_X=25.0
GL_WIDTH_IN_PIXELS=20

Note: some additional parameters might show up in automatically created files. These can safely be ignored as they do not have an effect for regular usage of MoMA.

The user properties file

In case you would like to use a specific setting you can

• put a file called 'mmuser.properties' into a folder '.moma' in your home folder.
• use the command line parameter '-p ' when starting MoMA. If a file 'mmuser.properties' (or the specified file) was found by MoMA, the console output will read like this:

Loading user properties from: /Users/maxmustermann/.moma/mmuser.properties
 >> user properties loaded!

You can overrule arbitrary of the parameters listed in the example properties file above. Lines starting with '#' are considered comments, allowing you to structure the user properties file for better readability.

# MoMA user properties -- just an example!
# A copy of this file can be put next to the data to analyze and set
# values can be used in IMM using the CLI parameter '-p' or '-props'.

# GrowthLine setup
GL_WIDTH_IN_PIXELS=20
GL_OFFSET_LATERAL=20
GL_OFFSET_BOTTOM=-1
GL_OFFSET_TOP=65

# GL detection setup
SIGMA_GL_DETECTION_X=15
SIGMA_GL_DETECTION_Y=0

# GL background removal setup
BGREM_TEMPLATE_XMIN=25
BGREM_TEMPLATE_XMAX=50
BGREM_X_OFFSET=50

# Tracking setup
GUROBI_TIME_LIMIT=25.0
GUROBI_MAX_OPTIMALITY_GAP=1.0
MIN_CELL_LENGTH=10
MOTHER_CELL_BOTTOM_TRICK_MAX_PIXELS=10

# Export setup
GL_FLUORESCENCE_COLLECTION_WIDTH_IN_PIXELS=100

Meaning of the individual exposed parameters

Parameters effecting background removal:

BGREM_TEMPLATE_XMAX=35
BGREM_TEMPLATE_XMIN=20
BGREM_X_OFFSET=35

For any pixel along a growth channel (GC), MoMA will take the average intensity of all pixels that lie between 20 and 35 pixel towards both sides of the detected GC center-line (shown in MoMA as a green line). This value will then be removed from all pixels that are up to 35 (BGREM_X_OFFSET) pixels away from the center line (in x-direction only).

One should make sure that the template parameters define a region well between two neighboring growth channels and that the offset parameters is chosen large enough to remove the background intensity for all GC pixels.

Path defining parameters

DEFAULT_PATH=/Users/maxmustermann

If MoMA opens file dialogs they will by default open in this folder. This parameter might be useful to save time navigating to a directory that is used often and hard to reach.

Growth Channel defining parameters

GL_OFFSET_BOTTOM=-1
GL_OFFSET_LATERAL=20
GL_OFFSET_TOP=50
GL_WIDTH_IN_PIXELS=20
GL_FLUORESCENCE_COLLECTION_WIDTH_IN_PIXELS=100

If GL_OFFSET_BOTTOM is set to '-1', the bottom of the GC will automatically be detected by MoMA. Any other value will set the GC bottom offset to precisely that many pixels (measured from the bottom of the images). The property GC_OFFSET_TOP does not offer the feature of being evaluated automatically and must be set to a positive integer value. The parameter GL_WIDTH_IN_PIXELS should be chosen to reflect the pixel with of the growth channel. The parameter GL_OFFSET_LATERAL is only affecting the width of the image as shown in MoMA. Choosing this value rather small will enhance the readability of exported tracking solutions (when exported as HTML). Fluorescent channels can leak the GC quite a lot. The parameter GL_FLUORESCENCE_COLLECTION_WIDTH_IN_PIXELS defines the with of the region around the GC center line in which the intensities are summed (prior to data export).

Parameters defining the window size and position of MoMA

GUI_HEIGHT=783
GUI_WIDTH=640
GUI_POS_X=2675
GUI_POS_Y=228
GUI_CONSOLE_WIDTH=600

Parameters affecting the solver (Gurobi)

GUROBI_TIME_LIMIT=15.0
GUROBI_MAX_OPTIMALITY_GAP=0.99

The value set for GUROBI_TIME_LIMIT defines the maximum time in seconds Gurobi is allowed to search for the optimal tracking solution. (After that, Gurobi will stop and the best solution found so far will be displayed.) GUROBI_MAX_OPTIMALITY_GAP defines the maximal multiplier allowed before the optimization would stop. A value of '0.99' means that Gurobi would only stop if the energy of the best found solution is at most 1.99 times the currently best known lower bound (energy is at most about twice the one of the optimum). Note: this value will overwrite the time limit and can cause Gurobi to solve significantly longer before terminating!

Defining the maximum time point for optimisation

OPTIMISATION_INTERVAL_LENGTH=-1

If this parameter is set to a value > 0, optimisation will only be done until this time point.

Cell segment properties

MIN_CELL_LENGTH=18
MIN_GAP_CONTRAST=0.02
MOTHER_CELL_BOTTOM_TRICK_MAX_PIXELS=10

Defines filtering options. All segment hypotheses shorter then MIN_CELL_LENGTH pixel will be removed before tracking. Similarly, all segments that are not divided by an intensity peak of at least MIN_GAP_CONTRAST height (in normalized intensity) will not lead to subcell segment hypotheses. The property MOTHER_CELL_BOTTOM_TRICK_MAX_PIXELS defines the number of pixels above GL_OFFSET_BOTTOM that would snug segments down to the bottom of the GC.

Image smoothing during MoMA startup

SIGMA_GL_DETECTION_X=25.0
SIGMA_GL_DETECTION_Y=0.0
SIGMA_PRE_SEGMENTATION_X=0.0
SIGMA_PRE_SEGMENTATION_Y=0.0

Sigma's in x and y direction that are used for temporary gaussian smoothing of the raw images during GC center line detection (SIGMA_GL_DETECTION_[X|Y]) and during segmentation (hypothesis creation).

Export options

EXPORT_USER_INPUTS=1
EXPORT_DO_TRACK_EXPORT=1

EXPORT_INCLUDE_HISTOGRAMS=1
EXPORT_INCLUDE_PIXEL_INTENSITIES=1
EXPORT_INCLUDE_COL_INTENSITY_SUMS=1
EXPORT_INCLUDE_QUANTILES=1

The default configuration for the export of analysis results can be entered here. Activate a checkbox by entering a 1 behined the equal sign.

Further questions? Feel free to contact me (Florian Jug)!