Software for the evaluation of laser-induced stripes in cell nuclei.
Negative Stripes

The method is described here:
Cells and Stripes: A novel quantitative photo-manipulation technique
Martin Mistrik, Eva Vesela, Tomas Furst, Hana Hanzlikova, Ivo Frydrych, Jan Gursky, Dusana Majera and Jiri Bartek,
Scientific Reports, to appear.

1. Copy the TIF files you want to analyze into the 'data' folder.
Single layer gray-scale TIFF files in 16bit depth are expected.
You are free to modify the software for different image formats.
The files must be named so that they are in the correct order, 
i.e. the first image is taken before the stripes are induced.
See the example in the 'Data' folder.

2. Run the 'ANeg_Segment_and_Track.m' routine.
The images will be segmented, individual nuclei will be identified and they will be tracked in time.
This may take some time (up to a minute per image).
You will be asked to set three parameters.
Unless you set them appropriately, the segmentation will not be very successful.
Preview of the segmented images will be written to the folder 'Preview'.
A single file 'segmentdata.mat' will be produced.
This file contains all the data on the recognized and tracked nuclei in all the images.
The routine 'BNeg_Evaluate_Stripes.m' reads this 'segmentdata.mat' file.
If you have your own ways of segmenting and tracking the nuclei, feel free to use them,
only make sure your segment-and-track results are in the same structured format as the data in 'segmentdata.mat'.
If you find it hard to understand the data format structure, please contact me at tomas.furst@seznam.cz.

3. Run the 'BNeg_Evaluate_Stripes.m' routine.
This routine will read the 'segmentdata.mat' file and all the images in the 'Data' folder.
Be careful, if you change the content of the 'Data' folder in the meantime, 'BNeg_Evaluate_Stripes.mat' will probably crash
because it expects that the 'segmentdata.mat' file contains info about the images in the 'Data' folder.
The routine will evaluate the measure of striation (see the article) of the individual nuclei at all time points
and produce several '*.csv' files and two figures which will be written into the 'Results' folder.
The '*.csv' files contain the following data:

	nucleus area, i.e. the number of pixels belonging to the particular nucleus at the particular time
	nucleus Signal Integrated Density (SID), i.e. the sum of gray-scale levels of pixels belonging to the particular nucleus at the particular time
	stripe area, i.e. the number of pixels in the part of the nucleus which is identified as a stripe
	stripe SID, i.e. the sum of the gray-scale levels of pixels in the part of the nucleus which is identified as a stripe
	measure of striation, i.e. the measure of striation (MS) of the particular nucleus at the particular time (see the article for the definiton of MS)

The rows of the *.csv files correspond to the recognized nuclei (each row one nucleus), the columns correspond to time points.
No headers are included in the *.csv files!

Figure 'MeasureOfStriationBoxplot.png' contains the boxplot of the MS values at all time points.
Note that the boxes are equidistant on the horizontal axis which usually does not correspond to the real spacing of the time points in your experiment.
This is to avoid unnecessary complications in reading the time points of your experiment.

Figure  'MeasureOfStriationLineplot.png' produces broken lines tracking the MS of each nucleus over time.
Note that unlike the boxplot, this figure makes use of the tracking part of the software.
This may or may not be needed in your experiment.

Both the figures may easily be produced from the 'MeasureOfStriation.csv' data by any data processing software.







