Measure
Based on the selection type, calculates and displays either area statistics or line lengths. Area statistics are calculated if there is no selection or if a subregion of the image has been selected using one of the first four tools in the tool bar. Calculates line length if a line selection has been created using one of the three line selection tools. Use the Analyze/Measurement Options to specify what area statistics are recorded.To export the measurements as a tab-delimited text file, use File/Save As/Measurements or select one or more lines (shift-click to extend the selection) and use Edit/Copy (C) or Edit/Cut (X). You can also save measurements by right-clicking (cmd-clicking) in the worksheet and selecting Save As or Copy from the popup menu.
Analyze Particles...
This command counts and measures objects in binary or thresholded images. It works by scanning the image or selection until it finds the edge of an object. It then outlines the object using the wand tool, measures it using the Measure command, fills it to make it invisible, then resumes scanning until it reaches the end of the image or selection. Type esc to abort this process. Use Image/Adjust/Threshold to threshold an image.Particles smaller than Minimum Size or larger than Maximum Size are ignored. Bins is the number of bins used for the particle size distribution histogram. Check Display results to have the measurements for each particle displayed in the ImageJ worksheet. Check Display Summary to display a summary that includes count, min size, max size, average size and total area. Check Show Outlines to display a window containing numbered outlines of the measured particles. Check Exclude Edge Particles to ignore particles touching the edge of the image. Check Size Distribution to display a particle size distribution histogram. Check Clear Worksheet to erase any previous measurement results.
Histogram
Calculates and displays a histogram of the distribution of gray values in the active image or selection. The x-axis represents the possible gray values and the y-axis shows the number of pixels found for each gray value. The total pixel count is also calculated and displayed, as well as the mean, modal, minimum and maximum gray value.For RGB color images, the histogram is of the combined red, green and blue channels. For 16 and 32 bit images, the range of gray values between Min and Max is divided into 256 bins.
Use the Save or Copy buttons to save the histogram data, formatted as 256 lines each containing a single number. Value:, which changes as you move the cursor, is the grayscale value corresponding to the x-axis cursor position and Count: is the number of pixels that have that value.
Set Scale...
Use this dialog to define the spatial scale of the active image so measurement results can be presented in calibrated units, such as millimeters. Before using this command, use the straight line selection tool to make a line selection that corresponds to known distance. Then, bring up the Set Scale dialog, enter the known distance and unit of measurement, then click OK. ImageJ will have automatically filled in the Distance in Pixels field based on the length of the line selection.Set Distance in Pixels to zero to revert to pixel measurements.
Setting Pixel Aspect Ratio to a value other than 1.0 enables support for different horizontal and vertical spatial scales, for example 100 pixels/cm horizontally and 95 pixels/cm vertically. To set the pixel aspect ratio, measure the width and height (in pixels) of a digitized object with a known 1:1 aspect ratio. Enter the measured width (in pixels) in Distance in Pixels. Enter the known width in Known Distance. Then calculate the aspect ratio by dividing the width by the height and enter it in Pixel Aspect Ratio.
Set Measurements...
Use this dialog box to specify which measurements are recorded by Analyze/Measure and Analyze/Analyze Particles.
Area - Area of selection in square pixels. Area is in calibrated units, such as square millimeters, if Analyze/Set Scale was used to spatially calibrate the image.Mean Gray Value - Average gray value within the selection. This is the sum of the gray values of all the pixels in the selection divided by the number of pixels. Reported in calibrated units (e.g., optical density) if Analyze/Calibrate (in v1.14 or later) was used to calibrate the image.
Standard Deviation- Standard deviation of the gray values used to generate the mean gray value.
Modal Gray Value - Most frequently occurring gray value within the selection. Corresponds to the highest peak in the histogram.
Min & Max Gray Level - Minimum and maximum gray values within the selection.
Centroid - The center point of the selection. This is the average of the x and y coordinates of all of the pixels in the selection.
Center of Mass - This is the brightness-weighted average of the x and y coordinates all pixels in the selection.
Perimeter - The length of the outside boundary of the selection.
Limit to Threshold - If checked, only thresholded pixels are included in measurement calculations. Use Image/Adjust/Threshold to set the threshold limits.
Show LUT
Displays a plot of the active image's lookup table. The lookup table, or color table, describes the color that is displayed for each of the 256 possible pixel values. A bar under the plot displays the color representation of the pixel values. Note that RGB color images do not use a lookup table.
Plot Profile
Displays a two-dimensional graph of the intensities of pixels along a line within the image. The x-axis represents distance along the line and the y-axis is the pixel intensity.For rectangular selections, displays a "column average plot", where the x-axis represents the horizontal distance through the selection and the y-axis the vertically averaged pixel intensity. To average horizontally, hold down the alt (option) key. Use the Save or Copy buttons to save the profile data, formatted as a sequence of lines each containing a single number.
Fractals>
This submenu provides access to various fractal analysis plug-ins.Gels>Save XY Coordinates...
Writes to a text file the XY coordinates of all black pixels in the active image, which must be 8-bit grayscale.Box Count...
Counts the number of boxes of an increasing size needed to cover a one pixel binary object boundary. The box size and the number of boxes necessary to cover the boundary are plotted on a log-log plot and the fractal dimension determined from the slope, i.e. D=-slope. For more information, see the "Fractal_Box_Counter.java" source file.
This submenu provides access to a plug-in that attempts to duplicate NIH Image's Gel Plotting Macros.Here is what you need to do to analyse a 2D gel:
| Plug-Ins Menu | Contents | Home |Note that there is currently no way within ImageJ to calibrate to optical density using step tablet standard.
- If the lanes are not horizontal, rotate the image using Image/Transformations/Rotate 90 Degrees Right.
- Use the rectangular selection tool to outline the first (top) lane.
- Select Analyze/Gels/Select First Lane (or press "1"). The message "Lane 1 selected" will appear in the status bar.
- Move the rectangular selection down to the next lane and select Analyze/Gels/Select Next Lane (or press "2"). The message "Lane 2 selected" will appear in the status bar.
- Repeat the previous step for each remaining lane. The message "Lane n selected" will appear in the status bar, where n is the lane number.
- Select Analyze/Gels/Plot Lanes (or press "3") to generate the lane profile plots.
- If necessary, use the magnifying glass tool to magnify and enlarge the window containing the profile plots.
- Use the straight line selection tool to draw base lines and/or drop lines so that each peak of interest defines a closed area. To get to all the lanes, it may be necessary to scroll the image vertically using the "Hand" tool. (Hold down the shift key to temporarily switch to this tool).
- For each peak, measure the size by clicking inside with the wand tool. If necessary, scroll the image by holding down the shift key and dragging.
- Select Analyze/Gels/Label Peaks to label each measured peak with its size as a percent of the size of the largest peak.