The ImageJ Updater is the best way to install and update plugins. Simply add the update site containing your plugins of interest, and they will be installed automatically for you. If the plugin is not available via update site, but packaged as .jar file, or as unpackaged directory with .class files, see Installing plugins manually below.
After completion of the registration process, the plugin uses the final position of the source and target landmarks to create a warped image that has the size of the target and that contains a distorted version of the source. The distortion is such that the landmarks of the source are mapped to those of the target. In the automatic and batch modes, the landmarks of the source have been refined to minimize the mean-square difference between the target and the warped image.
Fiji Manual Plugin Mac
The plugin can also be called by a macro or by another plugin. In the latter case, the registration can proceed silently if desired, and the registration results can be retrieved for further processing.
The plugin can accommodate grayscale images and RBG stacks. Only one color plane of the RGB stack is taken into account for registration; the transformation applied to the two remaining color planes will be adjusted accordingly.
Batch mode: the target image plays the same role in the batch mode as in the manual or automatic modes. If the target image is a stack, its second slice still defines a registration mask; else, every pixel of the target image is considered relevant. The source image, however, is treated differently. It has to be a stack for the batch mode to be enabled, and every slice gets registered in turn to the same target image. Each slice is given the same default mask, with every pixel being considered relevant. The output image that results from the registration process is returned as a stack. Each slice contains a warped version of the corresponding slice of the source image. As in the case of manual and automatic modes, the output type is float 32-bit. The batch mode is not available for RGB stacks.
In some situations, a single target is desirable because the source images differ essentially by their geometry, less so by their content. TurboReg is appropriate in those situations. But there also exist cases where the content of the several source images gradually evolves from frame to frame; this might happen for example with a time series, or with a 3D stack of slices that are acquired with only a loose control of the slice-to-slice alignment. A companion plugin has been written to help in this different settings; it is named StackReg and is available here.
You can choose one of two different trade-offs between registration speed and accuracy. When speed is favored, the output image suffers from low-quality interpolation (nearest-neighbor). Moreover, in the automatic registration mode, the accuracy is further reduced because the refinement of landmarks is made coarser. When accuracy is favored instead, the output image benefits from high-quality interpolation (cubic spline). Moreover, in the automatic registration mode, more effort is spent on refining the landmarks. Please note that it is not possible to perform automatic registration when speed is favored and when at least one of the dimensions of the target or source images is too small; in that case, manual registration is the only mode allowed (with the quality set to 'Fast'). Else, set the quality to 'Accurate'.
-transform 3) Given a set of landmarks, transform a source image. The details of the command are given in . This corresponds most closely to the manual mode of the interactive version of TurboReg. The quality is always set to 'Accurate'.
To call TurboReg from another plugin, we suggest the following Java statement: Object myTurboRegObject = IJ.runPlugIn("TurboReg_", myTurboRegOptions);where myTurboRegOptions is a String object that follows exactly the same syntax as described in the Macro case. Methods of the returned object myTurboRegObject can then be accessed thanks to a reflection mechanism. This approach facilitates code maintenance, especially the independence of all plugins; moreover, it limits the risk of having duplicate class names inside the hierarchy of folders spanned by ImageJ.
There are three public methods of interest inside the class TurboReg_. Those are getSourcePoints, getTargetPoints, and getTransformedImage. Typical calls look like: Method method = myTurboRegObject.getClass().getMethod("getSourcePoints", null); double[][] mySourcePoints = (double[][])method.invoke(myTurboRegObject, null); method = myTurboRegObject.getClass().getMethod("getTargetPoints", null); double[][] myTargetPoints = (double[][])method.invoke(myTurboRegObject, null); method = myTurboRegObject.getClass().getMethod("getTransformedImage", null); ImagePlus myTransformedImage = (ImagePlus)method.invoke(myTurboRegObject, null);where the necessary encapsulating blocks (e.g., try catch() ) have not been shown, for simplicity. The full description of these three methods and of their parameters is available from the API of TurboReg. A fully developed example of a plugin that takes advantage of the interoperability of TurboReg is StackReg.
MTrackJ was developed at the Biomedical Imaging Group Rotterdam of Erasmus University Medical Center in the Netherlands when I was working with colleagues on evaluating the performance of existing and newly developed tracking algorithms compared to manual tracking by human observers. Writing a general purpose program such as MTrackJ is not completely trivial. Therefore, if you publish results based on MTrackJ, I expect you to acknowledge me by citing the following paper:
The paper gives an overview of principles and software for cell and particle tracking in time-lapse microscopy images and mentions MTrackJ as a useful tool for manual tracking in case automated tracking methods fail.
The aim is to characterize the orientation and isotropy properties of a region of interest (ROI) in an image, based on the evaluation of the gradient structure tensor in a local neighborhood. The theoretical background is fully described in this PDF document. The software package OrientationJ automates the orientation analysis with four functionalities: performing a visual representation of the orientation of a image, creation of a vector field map, plotting the distribution of orientations, and detection of keypoints (Harris Corner). OrientationJ has also others tools: the manual measurement of the orientation and coherency in a ROI,the computation of the dominant orientation, the alignment of images based on the gradient structure tensor and some test images (chirp).
We provide a software OrientationJ to produce to visualize and to measure the orientation in the images. This software package is a series of plugin running on ImageJ, Fiji, or ImageJ2a general purpose image-processing package. ImageJ has a public domain licence; it runs on several plateforms: Linux, Windows, Mac OSX.OrientationJ Analysis: Full interface to access to all features of the structure tensor and create color survey.
OrientationJ Measure: Make measurement of the orientation and the coherency inside reion of interest.
OrientationJ Distribution: Build a histogram of orientations based on selected structures.
OrientationJ Corner Harris: Find corners in an image based the Harris corner detection.
OrientationJ Vector Field: Evaluate the direction by regular patches.
Test Image: Create a test image.
Installation
I have Fiji with ImageJ 1.51s. I tried creating a dummy dataset with the MRI Stack sample and got the same results (file has 0s when loaded through plugin but all data is there when opened in Excel). Updating did not solve the problem. Is this a bug?
Fiji features thousands of plugins that aid in scientific image processing and analysis. Here are a few featured plugins hand-picked by the Fiji community - refresh the page to see different plugins!
Note: For plugin versions lower than 5.5.7: Some Windows unzip apps create a double folder enclosing the plugin. If that is the case, copy the inner OMERO.imagej-5.x.x folder into Fiji.app > plugins folder.
This article introduces manual and automatic counting techniques using ImageJ, an open-source image processing program (Figure 1). Counts (e.g., number of leaves, fruits, seeds, or plants) are a common type of data gathered in horticultural research. In many instances, using ImageJ can increase the ease and accuracy of gathering count data. When image processing can easily separate objects of interest from the background, automatic counting with ImageJ can eliminate tedious manual counting processes. Furthermore, additional plant growth data, such as leaf area, plant width, and canopy area, can be collected from the same image. The image processing and analysis techniques introduced in this article are easily accessible and simple to use and thus can be adopted not only by researchers, but also by Extension agents and students. This article is part of a series introducing various image-based measurements with ImageJ for horticultural research. The tutorial video for this article is available at the UF IFAS Horticultural Crop Physiology Lab YouTube channel ( ). Other ImageJ tutorial videos are also available at =PL4qrjj3jZ6i568ToiUV-DvAsQ0Gyb30hK.
ImageJ is an open-source image processing program in which many custom plugins are available to solve various image processing and analysis problems. ImageJ can improve the ease, accuracy, and speed of count measurements in many cases. When image processing can easily separate objects of interest from the background, automatic counting with ImageJ is extremely fast and can eliminate tedious manual counting processes. When image processing for automatic counting is not feasible, counter tools in ImageJ can be used to facilitate easy manual counting. ImageJ is also capable of collecting various plant growth measurements, such as leaf area, plant width, and canopy area (Agehara 2020), allowing count and additional growth data collection from the same image simultaneously. 2ff7e9595c
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