Multicolor stack in imagej fiji3/9/2024 ![]() With ImageJ, you can crop a photo in order to create a specific size image using its crop tool. You just drag the crop area over the image’s portion you want to crop, then release the mouse button to do so. You can also crop by dragging and dropping. After selecting the area you want to crop, click OK. To crop an image in ImageJ 1.38 or later, press Shift-X and then move the cursor over a portion of the image you want to crop. To crop the image or stack, simply press shift-x. When an image is shifted to the right, it is easily cropped. The toolbar includes a scroll bar in the upper right hand corner that can be used to expand or shrink the crop area. ![]() Crop tools can also be found in the toolbar on the left side of the window. By dragging an image and dropping it, ImageJ offers two simple ways to crop it: shift-x (the process by which you crop by pressing shift-x) and drag-and-drop. Depending on your needs, you can crop an image using ImageJ. There are numerous reasons why you may want to crop an image you may be removing a section of the image or attempting to make another image from the one that already exists. Performance: the alignment of the 140 slices (and their resizing) took around 20 minutes in a 8-CPUs Intel Core Duo at 3.4GHz, 32GB of RAM, running on Linux 64-bit.You can crop a stack using the plugin plugins Stacks Crop (3D) after selecting ‘OK,’ which will reveal the panels of the ZY and XZ planes, as well as the original stack, which you can crop using the mouse. We then click on OK and the alignment starts.Īfter few minutes (depending on the computer and number of CPUs), when the alignment is done, aligned images are saved to the specified output folder and results will be displayed as a virtual stack. For more details about the parameters, visit the registration plugin page. NOTE: these values are usually a good choice, but they can be tuned when working with other types of images. Here, we only increase the steps per octave scale to 5 to find more point candidates to correspondences, and the maximum image size to 1400 pixels, to use more image information. When we click on OK, another dialog pops up to select the Feature extraction parameters: Since we chose translation, we don’t have this problem, but we checked this option anyways to guaranty a complete multi-thread registration. Shrinkage constrain, in other registration models, this guaranties a non-shrinking registration.Advanced setup, to specify the feature extraction parameters.The feature extraction and registration models: in this case, and as mentioned before, we only need a translation to model the transformation.Īnd we click on the first two check-boxes:.The output directory: we set it to the folder where we want to store the final aligned slices.The source directory: we set it to the stitching output folder so the plugins will align the stitched images.Alignmentįor the alignment of the stitched slices we will use the plugin Register Virtual Stack Slices, under Plugins › Registration:Īs before, a dialog will pop up where we have to choose the registration parameters: Performance: The stitching of the 19,600 images (732x732 pixels each) took around 117 minutes in a Intel Core Duo at 3GHz, 4GB of RAM, running on Linux 64-bit. The plugin will display all intermediate results until the whole sequence has been stitched.Īfter processing the last grid/section, the plugin will display the following message:Īs result, the stitched images are stored in the output folder: We then click on OK and the stitching will take place. The default value (0.3) is quite low, but in our test case works perfect. The regression threshold: the number below with the plugin won’t accept correlation values as valid.In our test case we won’t fusion the images, so we select None. The fusion method: the way the plugin will treat the overlapping areas.The output directory: the folder to store the resulting stitched images.All the images are stored in the same folder and have an intuitive sequencing name (such as Tile_X(xxx)_Y.png.The transformation between slices can also be modeled as pure translation. Given the origin of the images used in this tutorial, the transformation between tiles can be modeled as a pure translation to generate the mosaic (of a slice). This tutorial describes ’ how to produce an image stack (or 3D image) from an input sequence of tiles’ using the Fiji plugins for stitching and registration. If you’d like to help, check out the how to help guide! Introduction The content of this page has not been vetted since shifting away from MediaWiki.
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