6
Image 5D Data Display
Images captured through the “Acquire!” button are displayed with ImageJ’s Image 5D
plugin. This is a different way of displaying data from what most ImageJ users are used to, but it has
some nice features. If you don’t like Image 5D or it does not
meet your needs, your raw .tif images can be opened in
ImageJ with the File Import Image Sequence function,
which will display the standard ImageJ format. If you like
Image 5D, it can be downloaded to your own computer and
used to display .tif data from any microscope.
Basics of Image5D: Image5D is just a way to
display .tif data, it is not a special image format. All .tif files
acquired with the “Acquire!” button will be displayed with
Image5D, but will save as regular .tif files or .stk tiff stacks.
To add false color to a captured image, use the pulldown
menu to choose the “color” option. Red will be assigned by
default. To change this, hit the “Color” button on top of the
pulldown menu and select a color from the menu that pops
out of the right hand side. For timelapse images (and for z-stacks, if you open data from another
microscope) a slider along the bottom of the image allows you to flip through your time points and/or z-
planes. If you have volume over time, there will be two sliders, one for time and one for z. To save your
data, you must first “convert” it to a stack. From
the main ImageJ menu, choose Plugins Image5D
Image5D to stack. A regular stack should
appear (not in the Image5D-type window). This
can then be saved as a .tif stack, .avi movie
(Windows Media Player) or .mov movie (Mac
Quicktime). Both movie types should allow you to
set the playback speed (frames per second) and
compression upon saving.
If you open a .tif stack with multiple
colors or an RGB color image using Plugins
Image5D RGB to Image5D, Image5D will at
first only display one channel. You will be able to
flip through the color channels with the large grey
slider that appears under the pulldown menu. Choosing the “overlay” option from the pulldown menu
gives a merged image of all the colors in the sample, with the option of toggling individual channels on
and off with the checkboxes, and/or adjusting the color/brightness/contrast/etc. of a particular channel by
selecting that channel (fill in the dot next to the name). Before saving, you must select a “conversion”
method under Plugins Image5D. If you choose Image 5D to RGB, and RGB image will be created as
displayed, and then that image can be saved as a .tif or other file type with File Save As or File
Save. These files will open in ImageJ, PowerPoint, Photoshop, etc. If you choose Save As Image5D, the
file will be saved in the Image5D format and will only open with the Image5D plugin for ImageJ.
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