#Particle tracker imagej how to#
#Particle tracker imagej manual#

Select the Show: Outlines option to display an image of the detected objects. Roundness values between 0.0 and 1.0 can also be selected to help exclude unwanted objects. Set the minimum size and maximum pixel area size to exclude anything that is not an object of interest in the image. This will provide you with information about each particle in the image. To analyze the particles in a segmented image, use the menu command Analyze › Analyze particles…. This meeting point is where a watershed line is drawn. These points are then dilated until they touch another black pixel. These are the ultimate eroded points (UEPs) of each black area meaning they are equidistant from each edge. From this the centers of the objects are calculated. This is the Euclidian distance map (EDM) of the black area. Black pixels closer to the edge are lighter than black pixels that are more central. The black pixels are then replaced with grey pixels of an intensity proportional to their distance from a white pixel. Overlapping objects in a binary image can be separated using the menu command Process › Binary › Watershed.įirst convert the image to binary by thresholding.

For a complete list of the methods available with Fiji see the Plugins section located in the Documentation section under the Content tab at the top of this page. These include Otsu’s thresholding, maximum entropy threshold, and mixture modelling thresholding. An evaluation of over 40 of these can be found in this paper:įiji has several plugins found in the menu Image › Adjust › Threshold for automatic calculation of an image threshold. There are many algorithms you can use to calculate the threshold without introducing user-bias. The image can be converted to a binary image via the menu command Image › Type › 8-bit. The background of the thresholded image can be made light or dark. The Color space option allows you to choose between HSB, RGB, Lab, and YUV. The Threshold color option allows you to choose between Red, White, Black, or B&W as the thresholding color. The Thresholding method option allows you to choose a thresholding techniqe other than the default. You can also choose to check the Stack histogram box to produce a histogram for an entire stack.įor color images, setting the threshold is done with the command sequence Image › Adjust › Color Threshold…. The Dark Background box will flip the foreground color with the background color. The drop-down menu set to Red allows you to choose between a red on white color scheme, a black on white color scheme, or an over and under color scheme. The drop-down menu set to Default allows you to choose between Default and 15 other threshold techniques.

#Particle tracker imagej manual#

You have different options for setting a manual threshold. This will permanently apply the threshold settings and convert the image to binary. When you are satisfied with the threshold settings, you can then hit Apply. The pixels within the threshold range are displayed in red. The threshold can be set using the slider bars. Monochrome images are most simply thresholded via the menu command Image › Adjust › Threshold. There are several ways to set thresholds. All pixels in the image whose values lie under the threshold are converted to black and all pixels with values above the threshold are converted to white, or vice-versa. A threshold range is set to tell the objects of interest apart from the background. RAW Threshold Watershed “AnalyzeParticles” Setting a thresholdĪutomatic particle analysis requires a “binary”, black and white, image. Once this has been done, however, the object can then be analyzed.

Segmentation, or the ability to distinguish an object from its background, can be a difficult issue to deal with. Manual particle counting can be done using the Multi-point Tool.

#Particle tracker imagej how to#

If you’d like to help, check out the how to help guide! Automatic Particle countingĪutomatic particle counting can be done if the image does not have too many individual particles touching. The content of this page has not been vetted since shifting away from MediaWiki.