All of the results from the image processing steps are saved in the
zip file you downloaded. Several different types of analyses are
automatically done on each image set, below you will find a few
instructions on how to find a few of the most common properties
measured in focal adhesion dynamics experiments. You can also find
short descriptions of all the results files here as well.
Focal Adhesion Assembly and Disassembly Rates
The Focal Adhesion assembly and disassembly rates are stored in the
file named "ad_kinetics.csv" in the "adhesion_props" folder. These
results have been filtered to only include adhesions with positive
rates and p-values of less than 0.05. Four properties are reported
for each rate:
- class: Either assembly, disassembly or stability
- FA_number: This is a unique number assigned to each adhesion
during the tracking process.
- slope: This is assembly or disassembly rate calculated
using the same method as Webb, et al. 2004, with the
modifications described here
- p.value: The p value calculated for the likelyhood of
seeing the determined assembly/disassembly properties
occuring by chance.
- r.squared: This is the value of R² for the
log-linear line fit.
- image_count: The number of images included in the
phase.
- phase_length: The total realtime length of the phase in
minutes.
If you want to dig deeper into the results, visualizations of each
adhesion and the measurements of the intensity of the adhesion
marker at each image is also available. You can find the
visualizations in the "single_ad" folder in "visualizations", where
each file is named using the same number as appears in the ad_num
column of the results file.
You can see a graph of the intensity measurments and the
corresponding assembly or disassembly phase in the
Average_adhesion_signal.pdf file in the models directory of
adhesion_props. In this file, the title of each graph is the same
number as in the ad_num column. Finally, if you want the raw
intensity data, you can look at the Average_adhesion_signal.csv
file in lin_time_series. Each line of the CSV file corresponds
to a single adhesion, where the line number corresponds to the
ad_num column.
Focal Adhesion Stability Phase Properties
Several properties of the FA's stability phase are also measured
and saved. To be present in this file, the adhesion must have an
assembly and disassembly phase where the p-value of the
log-linear fit is less than 0.05. The image_count and FA_number
properties are the same as in the assembly/disassembly property
file. These properties haven't been used any publications, but
they might be of interest.
Some of the following values use a normalization scheme to
attempt to correct for differences in FA marker intensity. Thus
the normalized intensities values are found by dividing the
intensities of FA marker by the average of the first and last
intensity values in a given FA's intensity time series.
- mean_intensity: The average of the FA marker intensities
during the stability phase.
- mean_fold_change: Average of the normalized intensity
values during the stability phase.
- stdev: The standard deviation of the normalized
intensity values during the standard phase.
- coeff_of_var: Result of dividing stdev by
mean_fold_change values, the coefficient of variation.
- half_peak_time: Amount of time between the time when the
assembly phase hits half of the stability mean intensity and
when the disassembly phase hits half of the stability mean
intensity.
If you want to dig deeper into the results, visualizations of each
adhesion and the measurements of the intensity of the adhesion
marker at each image is also available. You can find the
visualizations in the "single_ad" folder in "visualizations", where
each file is named using the same number as appears in the ad_num
column of the results file.
You can see a graph of the intensity measurments and the
corresponding assembly or disassembly phase in the
Average_adhesion_signal.pdf file in the models directory of
adhesion_props. In this file, the title of each graph is the same
number as in the ad_num column. Finally, if you want the raw
intensity data, you can look at the Average_adhesion_signal.csv
file in lin_time_series. . Each line of the CSV file corresponds
to a single adhesion, where the line number corresponds to the
ad_num column.
Find Static FA Properties
Several different properties are collected about each focal adhesion
identified by the system. These properites, such as area and intensity
are stored in two ways: as single measurements associated the adhesions
in each image and as measurements over time associated with the
adhesions tracked through time. The single measurements are all in the
sub-folders of the "individual_pictures" folder, specifically the
"raw_data" folder. There you will find various csv files such as
"Area.csv" and "Average_adhesion_signal.csv" which contain area values
and intensity values respectively. All of the units of distance or area
are in pixels or square pixels.
Find Dynamic FA Properties
In addition to static properties collected by the system,
several dynamic properties are also collected. These properties
are summary properties of a single adhesion over time, even if the
adhesion was only present in the movie for a single frame. These
properties can be found in the 'single_lin.csv' file in the
'adhesion_props' folder.
The calculated properties include longevity (lifetime), largest
adhesion area, mean area, mean FA marker intensity and axial
ratio. If a cell mask set of files are provided, the average
distance from the cell edge and cell center are also included.
Find the Focal Adhesion Alignment Index (FAAI)
You can lookup the value of the FAAI in the
"adhesion_orientation.pdf" file in the "adhesion_props/FAAI" folder. The
value of the FAAI is reported in the title of the left hand plot in
the center row.
Files in adhesion_props
The "adhesion_props" folder contains a range of output files
describing the extracted and summarized properties of the FA.
The 'image_analysis' folder contains diagnostic plots and
intermediate files used in the image analysis stages of the
pipeline, I won't go into detail about these files. The rest of
the results, divided by folders, are as follows:
assemb_disassem_models
These files all relate to the assembly/disassembly models built
on the average FA marker intensity. If you are interested in the
rate information, see the above section. Otherwise:
- assembly_rows_lengths.csv: Simple file containing the FA
number and the length of the corresponding assembly phase.
Has been used in the visualization steps to produce small
multiple images of single adhesion assembly phases.
- disassembly_rows_lengths.csv: Same format as
assembly_rows_lengths.csv, but for the disassembly
phases.
- Average_adhesion_signal.Rdata: Intermediate data for the
rate models, formated for the R programming language.
- Average_adhesion_signal.pdf: Diagnostic images for the
rate calculations, shows all the assembly/disassembly phases
ploted with R-squared and rates.
FAAI
All of these files relate to calculating the FAAI and FA angle
measurements.
- adhesion_orientation.pdf: Diagnostic summary of the FAAI
calcuations. Upper left: Adhesion angles using positive
X-axis as the 0 angle. Upper right: FAAI values through the
angle rotation procedure, red line the average angle, blue
line the median angle, y-axis label for FAAI value. Middle
left: FA angles rotated to dominant angle. Middle right:
Dominate angle for each image taken individually. Bottom:
Histogram of the devation from starting angle for single
FA
- FA_orientation.Rdata: Intermediate data for calculating
the FAAI values, formated for the R programming
language.
- FAAI_angles.csv: The angles of the FA rotated to the
dominant angle, used to calculate the FAAI.
- per_image_dom_angle.csv: The dominant angle on a per image basis
lin_time_series
This folder contains sets of FA properties organized into
matrix format. Each data file is arranged in the same fashion,
on each row are the properties of a single adhesion and in each
column are all the properties from the adhesions present in a
single image. For the adhesions that haven't been born or have
died, NaN is used as placeholder value.
Several of the properties rely on the presence of a secondary
marker to use to find the boundary of the cell. These properties
aren't calculated when the secondary marker isn't present.
I also calculate the overall cellular centroids in two ways,
depending on the data available. When only an FA marker is
present, I calculate the "FA centroid", which is simply the
average of the x and y coordinates of all the FA found in the
image. When the secondary cell boundary marker is present, I
also calculate the "cell centroid", which is the unweighted
centroid of the pixels in the cell body.
- Angle_diff_from_radial.csv: The difference in angle between the line leading from the FA centroid to the individual FA major/minor axis angle.
- Angle_to_center.csv: The angle between the cell mask centroid and the individual FA centroid.
- Angle_to_FA_cent.csv: The angle between the FA centroid and the individual FA centroid.
- Area.csv: The area of the adhesion.
- Average_adhesion_signal.csv: Average value of the FA marker intensity.
- Centroid_dist_from_center.csv: Distance from the cell mask centroid to the individual FA centroid.
- Centroid_dist_from_edge.csv: Distance from the cell edge to the FA centroid.
- Centroid_x.csv: Location of the unweighted FA centroid x component as returned by regionprops.
- Centroid_y.csv: Location of the unweighted FA centroid y component as returned by regionprops.
- CHull_dist.csv: Distance from the convex hull edge to the FA centroid.
- Dist_to_FA_cent.csv: Distance to the FA centroid from the the individual FA centroid
- MajorAxisLength.csv: Length of the major axis of an ellipse fit to the adhesion.
- MinorAxisLength.csv: Length of the minor axis of an ellipse fit to the adhesion.
- Orientation.csv: Angle between the major axis and the positive X axis.
Finding a FA ID Number From the Visualizations
Suppose you have been looking at the FA highlight visualizations
in 'visualizations/tracking' and want to connect an FA you see
highlighted to the extracted data in the other results. In order
to do this, you need to find the FA ID number that uniquely
identifies that FA in the rest of the data files. The processing
pipeline produces a set of visualization files that mirror the
files in 'visualizations/tracking', but have FA ID number labels
on each FA.
The FA ID visualization files are located in
'visualizations/lineage_id' and require another program that can
read svg files in order to see the ID labels associated with
each FA. I've tested these files in
inkscape, which is open
source and free, but I expect Adobe Illustrator would also work.
With the FA ID files located, you can now open an '.svg' file
which contains your adhesion of interest and you should see
something like this:
To find the FA ID, you need to zoom in until the tiny labels
associated with each FA are visible. In inkscape, you can hold
down ctrl and use the mouse wheel or the 'View/Zoom' menu to
zoom. After zooming, you should see something like this:
Although the ID numbers aren't the easiest to read,
especially in areas of dense FAs, the ID numbers will always be
to the lower right of each FA. I had to make the ID numbers that
small to make it possible to see the numbers without too much
overlap. You can double check the ID number by opening another
svg image from the folder, which also contains the same
adhesion. This is the same ID number used in all the files in
'adhesion_props'. It also corresponds to the row number in the
'lin_time_series', so if you find your FA ID number is 1000, all
the row number 1000s in csv files in 'lin_time_series'
corresponds to your FA.
By the way, this solution isn't all that great, but I'm open
to other ideas on how to link from the visualizations to the raw
data. Feel free to get in touch with me if you have any ideas.