The file (Spindly-GFP.zip) is a TIFF stack contained in a ZIP archive. It has 2 channels, 24 slices and 7 frames. A large part of the GFP fluorescence is bleached in the second frame and the cells go through mitosis, later. In consists of HeLa cells with an H2B-GFP construct to stain the chromatin imaged in fluorescence and transmission. Display changes in overlay mode are SLOW.Ī sample 5D data set is available.Converting the type (8-bit, 16-bit, float) does not work.Saving just saves the current stack, not the full dataset.Stack to Image5D converts an already opened stack to an Image5D, and RGB to Image5D converts an RGB image or stack to an Image5D. Open Series as Image5D opens a series of images or stacks from hard disk and converts it to an Image5D. To create an Image5D, use the plugins “Open Series as Image5D”, “Stack to Image5D” or “RGB to Image5D”. In the one channel color and overlay modes one can open a panel to select the display color of a channel or to edit a more refined LUT with the ImageJ LUT Editor. Options are one channel in gray, one channel in color and an overlay of selected channels. A dropdown menu allows to change the display of the channels. Image5Ds are displayed in a window with two scrollbars for slice and time below the image and a panel with controls to change the current channel and its color to the right of the image. That way plugins working on stacks should usually work as expected on the currently displayed stack of an Image5D (just try a z-projection to see what this means). Unlike the HyperVolume Browser, an Image5D has a “true” 5D format. These plugins extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t). If you do not wish to enable the Fiji update site, you can download the Image5D JAR file to the plugins folder, restart ImageJ, and there will be new commands ( New Image5D, Open Image5D, etc.) in the Plugins › Image5D submenu. Image5D is distributed as part of Fiji, so no installation is necessary beyond that. Please consider using the built-in hyperstacks functionality in ImageJ, since it is newer and more well-integrated than this old Image5D plugin.
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