toolbar. Here, define new start and end points of the series using the Start Slice and End Slice
sliders/data fields, or enter a value in the Every n-th Slice field if you would rather create a subset of
every n-th slice of your choosing.
3-D Projection
The Projection function can render a single projection or a series of calculated projections at set
angle increments around the X, Y, or Z axis. The user can choose between manipulating aspects of
the projection's transparency or creating a projection that has maximum intensity.
The "Transparent" projection method decreases the brightness of each file in the projected stack to
reveal structure in subsequent layers that would otherwise be hidden. The "Maximum" projection
method takes the intensity values of individual pixels in all sections and collapses them into one
single illuminated image. The "Maximum" method is chosen when the maximum pixel intensity is
desired to be represented in the projection.
Creating a maximum projection is described here. These instructions assume that an image stack is
open and therefore available for projection.
1. Select 3D View> Projection from the main menu. The Projection window will open.
2. Select the stack to be projected in the Source panel of this window.
Only stacks and images that are currently open are available for selection in the Source pulldown
list.
3. To create an en face (straight-on) projection of all slices in the z-axis, select the Y radiobutton in
the Projection panel. Leave the First Angle set to 0 degrees, enter 1 in the Number Projections
field, and set the Difference Angle field to 0 degrees.
4. In the Transparency tab, select the Maximum radiobutton.
5. Generate the projection by clicking Apply located in the upper right corner of the Projection
window.
6. If a sequence of projections at set angles has been created, it may be animated or viewed in a
gallery via the Select and Display toolbars of the image window.
Exporting Files to .tif Format
Files can be exported in a couple of different ways - via the batch export macro, which allows the
simultaneous export of multiple database items or the Export of Images function, which allows the
export of individual database items - be they single confocal sections or a stack. The Export of
Images method is described here.
1. Open your database and load (open) the file you would like to export.
2. Select File >Export from the main menu. The "Export Images and Data" window will open.
3. In the Save In field, designate to which drive or directory the exported data should be saved.
4. Enter a name for the exported image or series of images in the File name field.
5. In the Save as type field, select the image format into which the file should be exported.
When selecting an image format, pay heed to whether you are exporting a single confocal image or
a series (stack) of confocal images. Various image formats are supported (e.g. .bmp, .jpg), we
recommend TIF (.tif) format as it is lossless and widely usable.
For multi-channel images, you have the option of exporting individual color channels of data in
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