Biology Reference
In-Depth Information
can also use the adaptive gain and threshold to change both
continuously, trying to keep the dynamic range constant.
2. If your microscope already creates TIFF images, you should
be able to load them into MorphoGraphX (just drag and drop
the fi le into the MorphoGraphX window). In some cases, the
voxel size is not read correctly. If this happens, MorphoGraphX
includes a stack process called “Change Voxel Size,” in the
“Canvas” folder. In this process, you specify the size of the
voxel. If any dimension is set to 0, it won't be modifi ed.
3. The terminal window of MorphoGraphX is really important.
You should never close it. Closing this window will close
MorphoGraphX without any hope of saving anything. Also,
many algorithms provide more details on the processing or
warnings/errors in the terminal window.
4. When acquiring 12 bit images (and sometimes 8 bit), some
microscopes store the information in the least signifi cant bits
of each voxel, leading to a very dark image. The image needs
to be normalized to use the whole range of values. Use the
stack process “Autoscale Stack” in the “Filters” folder. You
can achieve a similar result without editing the image. First,
tick the “16bit” checkbox next to the “Main” checkbox.
Then, click on the rainbow button, and click the “Auto
Adjust” button. You can then apply the result of this change
using the stack process “Apply Transfer Function” in the
“Filters” folder.
5. To observe the internal parts of a sample, MorphoGraphX
provides clipping planes. There are three clipping planes, each
made of two parallel planes. The clipping planes are setup in
the “View” tab (Fig.
1i
). When enabled, only what is between
the two planes is displayed. Clipping planes can be moved by
fi rst selecting it in the “Control-Key Interaction” box in the
“Main” tab and using the mouse while pressing the “Control”
key on the keyboard. The distance between the parallel planes
is set by the slider placed on the clipping plane tab.
6. The transfer function is defi ned per store and can be edited
using the rainbow button placed under the checkbox of the
corresponding store. The transfer function dialog box shows a
histogram of the image, colored with the colors used in the
image (Fig.
1g
). The simplest way to use the transfer function
dialog box is to select a predefi ned transfer function from the
list and use the “Auto Adjust” button to optimize the transfer
function to the effective range of values of the image. For a
fi ner control, on the top of the histogram, you can see trian-
gular ticks (on most transfer functions, there are only two: on
the extreme left and extreme right). Each tick corresponds to
a defi ned color. In between ticks, the color is linearly interpo-
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