Read 4-byte int with Intel (little-endian) byte order (note: RandomAccessFile.readInt has other byte order than AVI)

Returns an ImageProcessor for the specified slice of this virtual stack (if it is one) where 1<=n<=nslices. Returns null if no virtual stack or no sli

This method closes all ImagePlus.

returns a string of a four-cc code corresponding to an int (Intel byte order)

Returns the image width of the virtual stack

Returns the image height of the virtual stack

This method counts spermatozoa located in the circle with center (x,y) and radius r, which are contained in tree @param x @param y @param r @param tr

Find the next position of fourcc or LIST fourcc and read contents. Returns next position If not found, throws exception or returns -1

@param theTracks - 2D-ArrayList with all the tracks @return 2D-ArrayList with all the tracks that have passed the filter

@param path @return

@brief This method add to the given JPanel a button with the specified parameters @param label - String that is shown as button's labe

@param imp ImagePlus This functions converts imp to grayscale.

@param impOrig @param impTh

@param imp ImagePlus @return 2D-ArrayList with all cells detected for each frame

@param s - Cell used as reference to calculate the distance @return euclidean distance to the Cell s

This method returns the class attribute MAX @return

@param path @return

This method sets the first image on the list and show it on screen.

Write an intData RGB value converted from YUV, The y range between 16 and 235 becomes 0...255 u, v should be between -112 and +112

@param options @param question @param title @return

@param imp @param spermatozoa

@param points @param wSize @return

@return

@param track - a track @return VCL (um/second)

@param imp ImagePlus This functions converts imp to grayscale.

@param source - Cell to be copied

This method draws on the image ip the heat map using accumulation in AC and the scale conc @param ip @param AC @param conc

This method returns a matrix[width][height] with the accumulation in pixel window W with radius r @param width @param height @param r @param tree @pa

@param analysis @param path @return

Process the first image and show it on screen

Read a single byte

@param imp @return

@param center @param maxSize @param displacement @return

@param path @return

This method counts, for the given set of trajectories, how many angles go in the gradient direction and how many in the opposite (or other) direction,

This method returns an array with the same components as the maximum accumulation found, it use the LUT to set the max and min, and the rest colors ar

/ @param imp

@return

Update cell count with new disolution d @param d

This method sets the first image on the list and show it on screen.

This method returns the area of the circumference sector with radius r and height h @param r @param h @return

This method calculates the average motility values for the given trial. @param rt - ResultsTable where the motility information will be adde

This method calculates the CH-index for the given set of trajectories. @param theTracks - 2D-ArrayList with all the tracks @return Ch-Index

This method calculates the individual motility values for the given trial. @param rt - ResultsTable where the motility information will be a

This method calculates the SL-index for the given set of trajectories. @param theTracks - 2D-ArrayList that stores all the tracks @return SL

This method counts, for the given trajectory, how many angles go in the gradient direction and how many in the opposite (or other) direction, dependin

This method refreshes the showed image after changing the threshold with the sliderbar

@param dir @return

@param cells @return KDTree array containing each cells component

Returns the number of images in this virtual stack (if it is one)

@param track @return

This method set a unique identifier for each spermatozoon in the spermatozoa list

@param filename @return

This function checks if the point(x,y) is in the range [s2.x-s1.x,s2.y-s1.y] beeing s1-s2 a segment

@return an array with only one ImagePlus, compatible with the input specification of other functions

@param track @return

Read 2-byte short with Intel (little-endian) byte order (note: RandomAccessFile.readShort has other byte order than AVI)

Read type of next chunk that is not JUNK. Returns type (or 0 if no non-JUNK chunk until endPosition)

Parameters dialog, returns false on cancel

This method choose between autoThreshold or apply a particular threshold to the given ImagePlus depending if this value has been set before or not. @

This method runs the correct analysis looking at the analysis variable set by the user. @param controls - control trials @param tests

This method counts, for the given set of trajectories, how many angles go in the gradient direction and how many in the opposite (or other) direction,

This method deselect all spermatozoa.

@param x1 @param y1 @param x2 @param y2 @return

@param imp @param theTracks 2D-ArrayList with all the tracks

@param imp @param impTh

Equalize imp histogram @param imp

This method search in the given set of trials for the one with the given ID. @param id - Identifier of the trial to find. @param trials

@param cell

@param id @param spermatozoa @return

@param impOrig @param analysis @param trialID @param trialType @param relativePath @return

This method returns all trials extracted from the given set of AVI files. @param filenames List of avi filenames to be analysed. @return All