For some measures, the sample size for a track, that is the number of valid point measurements available for the track, may be less than the total number of points in the track.
For example, there is no speed measurement for the first point of any track marked by NA in the point measurements window shown below , and hence the sample size for computing the speed statistics of a track is one less than the number of points in the track. Display cluster measurements: Option to display or hide cluster measurement results.
The corresponding results window displays for each cluster the minimum, the maximum, the mean, and the standard deviation of all point measurements for the cluster for those measures for which these statistics make sense. In addition, it displays the number of tracks and points in each cluster, as well as the minimum, the maximum, the mean, and the standard deviation of the durations and the lengths of the tracks in the cluster. For each measure except duration and length , the mean and the standard deviation of a cluster are computed as the weighted mean and standard deviation of the corresponding track measurements, where the weight for each track is equal to the number of points in the track.
This is the same as computing the uniformly weighted mean and standard deviation of the pooled point measurements. Display assembly measurements: Option to display or hide assembly measurement results. The corresponding results window displays for the entire assembly the minimum, the maximum, the mean, and the standard deviation of all point measurements for those measures for which these statistics make sense.
In addition, it displays the number of clusters, tracks, and points, as well as the minimum, the maximum, the mean, and the standard deviation of the durations and the lengths of all tracks in the assembly. The assembly mean and standard deviation of any measure except duration and length are computed from the pooled point measurements. The mean and standard deviation of the duration and length measures are computed from the corresponding pooled track measurements.
Include all tracks in measurements: Option to include all tracks in performing measurements. If not selected, measurements are performed only for tracks that are visible at any time point , excluding hidden tracks and tracks that are not visible in the present channel. Maximum decimal places: The maximum number of decimal places with which floating-point numbers are displayed in the result windows. That is, numbers that would require more decimal places for exact representation, are rounded to the specified number of decimal places.
Pressing the OK button in the measurements dialog starts the selected measurements. The result windows are automatically put to front every time this button is pressed. At any time, the result windows along with the main dialog and the log window can also be put to front by pressing the F key on the keyboard when the image window is active. An example of a point measurement results window is given below. The resulting tab-delimited file can then be imported in any spreadsheet program.
This quantity is not displayed if there is only one cluster and the user has deselected the displaying of cluster and assembly measurements. The pixel width and unit of length used here can be set as described above. The pixel height and unit of length used here can be set as described above.
The voxel depth and unit of length used here can be set as described above. This quantity is not displayed in the case of 2D image sequences. The frame interval and unit of time used here can be set as described above. This quantity is not displayed if there is only one channel. I [unit]: The calibrated image intensity value at the point. For 8-bit and bit images, the intensity calibration function and value unit can be set if necessary as described above.
Len [unit]: The length of the track from the start first point of the track to the current point inclusive. Thus the value of this quantity for the end last point of a track equals the total length of the track.
The pixel calibration and unit of length used here can be set as described above. D2S [unit]: The distance from the start first point of the track to the current point.
Thus the value of this quantity is always less than or at most equal to the value of Len. D2R [unit]: The distance from the current point to the reference point see the description of the Refer button for information on how to set the reference. D2P [unit]: The distance from the current to the previous point of the track. The pixel size and unit of length can be set as described above.
This quantity is computed as the magnitude of the most recent displacement vector pointing from the previous point to the current point of the track , divided by the frame interval. The pixel calibration, unit of length, frame interval, and unit of time can be set as described above. The pixel calibration can be set as described above. Measurements for which no sensible value can be determined are marked by NA.
All graphical objects track points, connecting lines, ID numbers are displayed in overlay mode and never become part of the original image data. Pressing the button starts the module for generating a movie RGB-color type containing the frames with the tracks drawn into them. Thus the resulting movie is a "hardcopy" of what you see when moving the time index scroll bar of the original image window. The track displaying behavior is highly configurable see the description of the Displaying button.
Note that in the case of multi-channel 3D image sequences, it is naturally impossible to display the correct slice and channel for all track points at the same time index, if there are multiple tracks.
Therefore, the slice and channel indices used for movie generation in such cases are fixed to the values of the image window at the time the button is pressed.
The only exception to this rule is when there is only a single track. In that case, since there can be only one point per time index, the resulting movie will display the slice and channel corresponding to each point. By default, the generated movie has the same duration number of frames as the input image sequence. However, keeping if the Ctrl key down while pressing the button opens the dialog below, which allows to refine the movie.
Trim movie to all-first and all-last track points: Option to delete or keep the leading and trailing frames of the movie that do not contain track points. Drop frames for which there are no track points: Option to delete or keep all frames of the movie that do not contain track points. The movie production module runs in a separate thread in order for ImageJ to remain responsive. It is, however, not possible to edit tracks or their displaying settings during movie production. The final set of buttons allow configuring the tracking, displaying, and general program behavior, and opening this online manual.
Opens the dialog below for configuring the tracking behavior of the program. The selected tracking options are activated when pressing the OK button of the dialog. They are also stored in ImageJ's preferences file and loaded when restarting the program. Move to next time index after adding point: Option to let the program automatically move to the next time index after adding a track point.
If the Shift key is down during tracking, it will move to the previous rather than the next time index. Time step size: The step size in frames used by the program in moving to the next or previous time index. This must be an integer number but may be positive to move forward in time or negative to move backward in time. Finish track after adding point at last time index: Option to let the program automatically finish terminate a track after adding a point in the last by default or the first when the Shift key is down frame of the image sequence.
Reset time to last start index after finishing track: Option to let the program automatically return to the time index corresponding to the firstly added point of a track, after finishing the track. Apply local cursor snapping during tracking: Option to let the program automatically pick the position of the specified image feature within the specified window around the current cursor mouse pointer position, rather than the cursor position itself, when adding a track point.
This option can be temporarily switched off during tracking by keeping the Ctrl key down when the image window is active. Snap feature: The image feature to snap the cursor to. Currently this can be either the highest Maximum intensity or the lowest Minimum intensity value within the snap window, or the intensity-weighted mean position of pixels having a value above Bright centroid or below Dark centroid a certain threshold. The threshold, which is automatically computed, is the value that maximizes the interclass variance between object and background pixels also known as Otsu's threshold.
Note that snapping operates on the original image intensity values it ignores possible intensity calibrations. During tracking, the position of the selected snap feature is indicated by a second, smaller crosshair cursor in highlighting color , next to the normal cursor. Snap range: The size in pixels of the window within which the program searches for the snap feature position.
During tracking, this window is indicated by a dotted square in highlighting color around the cursor position. The currently supported window sizes range from 3x3 to 51x51 pixels. The size always consists of odd numbers to have an equal number of pixels on either side of the pixel corresponding to the current position. Opens the dialog below for configuring the displaying behavior of the program.
The selected displaying options are activated when pressing the OK button of the dialog. Display reference: Option to display or hide the reference point, if set see the description of the Refer button for defining the reference.
Display active track: Option to display or hide the currently active not yet finished track. Display finished tracks: Option to display or hide the finished tracks. This may be helpful if you do not want to be distracted by these tracks while creating a new track. Visibility: Determines which part of the tracks is visible. This can be the Entire track tracks are always drawn from start to end point, regardless of the current time index , or Up to current time tracks are drawn up to and including the current time index , or From current time tracks are drawn starting from the current time index until the end of the track.
The latter mode may be useful in time-reversed tracking applications. Coloring: The coloring scheme used for drawing tracks. Tracks can be drawn with a different color Per track , or with the same color Per cluster , or all with the same Monochrome color.
In each mode, the visible color of an object track, cluster, all can be changed as needed see the description of the Color button. Note that the program has a limited color palette, currently consisting of different colors gray values not included.
If there are more than this number of objects requiring a color, the program will start reusing colors. Fiji is a distribution of ImageJ which includes many useful plugins contributed by the community. Published Delete. Add to story or collection; Share on Twitter; The next video is starting stop. FileDialog - ProgramCreek. Quote saved. View saved quotes Close. Login to quote this blog Login Close.
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See the release notes for information on the present and past versions. Copyright C Erik Meijering. Permission to use this software and corresponding documentation for educational, research, and not-for-profit purposes, without a fee and without a signed licensing agreement, is granted, subject to the following terms and conditions.
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