Results table

Plugin outputs results to the regular Results table of ImageJ. Meaning all of its functionality is preserved (like building distributions/histograms of columns, etc). It can be saved and loaded using regular ImageJ interface.

Results can be in two formats: results of detection and results of fitting. Since the number of returned parameters in these two methods is different, so is the number of columns. Table format for detection is kind of self-explanatory. So on this page only values of fitting output would be explained.

X_(px)

X coordinate of particle in pixels of original image derived from fitting.

Y_(px)

Y coordinate of particle in pixels of original image derived from fitting.

Frame_Number

Well, frame number where particle was found (actually, slice number). It uses "straight-through" enumeration of frames, meaning if you have a Hyperstack with multiple z, color, t, it would order them and assign numeration unique to each frame.

X_(nm)

X coordinate of particle in nanometers derived from fitting.

X_loc_error(nm)

Localization error of X coordinate of particle in nanometers derived from fitting. It is estimated using covariance matrix.

Y_(nm)

Y coordinate of particle in nanometers derived from fitting.

Y_loc_error(nm)

Localization error of Y coordinate of particle in nanometers derived from fitting. It is estimated using covariance matrix.

Z_(nm)

Z coordinate of particle in nanometers [derived](Calculate Z values) from astigmatism [calibration](Make Z calibration).

Z_loc_error(nm)

Prrecision of calculation of Z coordinate of particle in nanometers [derived](Calculate Z values) from astigmatism [calibration](Make Z calibration) (to be implemented).

Amplitude_fit

Amplitude of 2D Gaussian derived from fitting. In camera/image counts.

Amp_error

Fitting error of Amplitude parameter.

BGfit

Offset of 2D Gaussian corresponding to the background level. In camera/image counts.

BGfit_error

Error of fit of offset of 2D Gaussian corresponding to the background level.

SD_X_(nm)

Standard deviation of fitted 2D Gaussian in X direction in nanometers.

SD_X_error(nm)

Error of fit for SD_X parameter in nanometers.

SD_Y_(nm)

Standard deviation of fitted 2D Gaussian in Y direction in nanometers.

SD_Y_error(nm)

Error of fit for SD_X parameter in nanometers.

False_positive

This parameter is nominal, it marks particles deviating from expected shape. If fitted standard deviation of particle in X or Y deviates by 30% from the value of SD of PSF specified in "Detection Particles", it is marked as 1 (i.e. false positive). Otherwise the value is 0, i.e. "true positive".

IntegratedInt

Integrated intensity of particles with subtracted noise. Fitting is NOT used for calculation of this parameter. It is a sum of all pixels intensity in the square around spot, minus average background value estimated from the pixels at the perimeter of the square. The size of the square is equal to 3 times SD of PSF.

SNR

Estimation of Signal-to-Noise ratio for the specific particle. It is defined as Signal value divided by Noise. If the fitting is successful then the Signal is equal to Amplitude fit parameter. If not, it is equal to the maximum intensity value of the square around spot minus average value of background. Average background value is calculated using border of the square with size of 3 times SD of PSD. Standard deviation of background pixels gives Noise value.

R2_fit

R2 or R squared or coefficient of determination, parameter from 0 to 1, describing "goodness of fit". The larger the value, the better the fit.

Iterations_fit

Final number of iterations calculated during fitting.

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After usage of Link Particles to Tracks module to create tracks, additional columns are added to table:

Track_ID

Unique number of track

Particle_ID

Number of particle in the specific track

Track_Length

Total number of particles in tracks (not frames!)

Reverse_numbering

Particle_ID value counted in reverse: from track's end to beginning