Simply download the latest version and extract it to the Fiji or ImageJ2 plugins directory. Slide Set can be installed manually in Fiji or ImageJ2.
Click Install then Apply changes, and restart Fiji.Select the file that appears in the list ( slideset-core- version.jar).From the "View Options" list at the top, select View files of the 'Slide Set' site.Once the updater dialog opens, click the Advanced mode button.Make sure Slide Set is marked for installation:.Slide Set should appear in the Plugins menu.Īnd that's it! From now on, running the Fiji updater will also check for Slide Set updates, and install them if they are available. Make sure the box at the left is checked.
Scroll to the bottom of the list of available update sites.Select the Manage Update Sites button at the bottom-left of the updater window.Start Fiji and run the updater ( Help > Update Fiji).Note: If you don't have the Fiji distribution of ImageJ, you can download it here. It's also possible to install Slide Set manually in Fiji or ImageJ2. The easiest way to use Slide Set is to install it in Fiji using the Fiji updater. Slide Set will not work with plain ImageJ. Specifically, it requires either an up-to-date version of Fiji or the latest release of ImageJ2. Name of the output directory (currently, “vecdata”).Slide Set is a plugin for ImageJ, so naturally it requires ImageJ.change the file name of the image stack.change the path to the image containing folder.More frames for averaging results in less noise. In other image sequences, this value could be larger depending on the result of running averaging. We use the sample image eb1_8bit.tif in the following workflow. This preprocessing averages several framed before and after the current frame, and will reduce noise in background to have a smooth image sequence, which is better for detecting optical flows / movements. For this, install Running Z Projector written by Nico Stuurman. PIV plugin: as the PIV plugin depends on OpenCV library, please read the installation section of the PIV plugin website carefully and follow the instruction.įor most type of time-lapse sequences, preprocessing the sequence by running average (also called “box averaging or moving averaging”) is recommended.These results are saved in the folder declared in #3 above.
The full path to which should be directly written in the script (see Usages).ĭisplacement vector fields as sequence of images. For more details, see the plugin site.Īn image stack. The script presented here is an add-on for Qing Zong Tseng’s PIV plugin, to batch process multiple images and outputs a sequence of vector fields. I implemeted the gradient method as a Igor Procedure and is available for downlaod: Vec2D package. One ImageJ plugin is available that implements the gradient method (generally called optical flow): FlowJ (or also see for a link to github repo). This PIV plugin takes two 2D images and estimate the displacement vector field between two time points.
Two ImageJ plugins use the cross-correlation methods: one by Jean-Yves Tinevez ( PIV analyzer), and another one by Qing Zong Tseng ( PIV plugin). Two different algorithms are known for the computation of vector field: the gradient method and the cross-correlation methods. The results are typically presented as a vector field, where movement vectors are plotted at regular intervals in the image. Particle Image Velocimetry (PIV) is a way of quantifying speed and direction of movement occurring within video sequences.
IJscript PIV Speed Measurement Vector Field