- Why is it so hard to align my sections in blend mode?
-
Difficulty in blending images can be caused by low contrast.
If your images have low contrast,
try using the Contrast Dialog in IGL Trace (from the Section menu) and
selecting the Equalize check box. Then save the result using
Section->Save Image. The result should be improved contrast when you
reload these sections into IGL Align.
Another common problem with using blend to align sections occurs when
sections are relatively thick.
If there are relatively few features that are the same in each section,
the blended images always look blurry even when they are
aligned. If possible try an alignment using thinner sections and see
if the alignment process isn't easier.
- Why can't I flicker rapidly between images in IGL Align?
-
Flicker is one of the hardware accelerator features that does not
work in IGL Align without the appropriate hardware.
Flicker relies on swapping of image buffers as implemented
in the SWAP_EXCHANGE mode of the OpenGL graphics standard.
If you have installed IGL Align onto a machine without an
OpenGL (3D Graphics) accelerator, flicker will definitely NOT
work properly because Microsoft did not implement buffer swapping in
the software version of OpenGL.
Sadly, a lot of OpenGL hardware vendors have followed Microsoft's
limited OpenGL implementation. If you think you have OpenGL
hardware installed, consult the 'System Requirements' of Align's
Help to see if it is compatible. If it might be, follow the
procedure described in the section on 'How to initialize Align'
to try to find a display mode with SWAP_EXCHANGE enabled.
Because of the limitations of the existing (partial) OpenGL
implementations, I have written a new program called SEM Align
which does the alignment and flickering without OpenGL or special
purpose hardware. To get this program, go to the software tools
page on our website.
You may be able to get better flicker in Trace by holding down the "/" key.
It may be helpful to save the approximate alignment in Align and then switch to
Trace to do the flicker.
- Okay, so I can't flicker without the proper hardware.
How can I get the two images to stop flickering (once) and just display image2?
-
Again, this is symptomatic of the Microsoft's software implementation of OpenGL,
but here's a work around:
- Open the Current Transform dialog from the IGL Align Commands menu.
- After aligning in blend mode, switch to flicker mode by hitting page up.
- Copy the Current Transform.
- Restore Image2 from the Commands menu.
- Paste into the Current Transform and Apply it.
- When I load a new image the display becomes completely bleached out. What happened
and how can I undo this bleaching?
-
The problem with the bleached images is caused by loading from a file while the display
is in blend mode. If you first switch to non-blended display (flicker), then load the
file, the bleaching does not occur. But once the bleaching has happened you can't fix
it by exiting blend mode and reloading -- it stays screwed up.
If you accidentally load a file while in blend mode, try hitting the "-" key on the
numeric keypad once. Sometimes this restores the balance.
- In trying to use blend, I put an image of one color in one
image buffer and an image of another color in the other buffer.
IGL Align converted them to the same color. Any reason why it has to do that?
-
Both images are displayed using the same color palette, so unless they
have the same palette to begin with one image will be switched to
the other's palette. If your images use a continuum of shades of one color, it
is unlikely that you can get this same continuum for two different
colors in one 8-bit color palette.
- You are recommending the Oxygen 402 board for IGL Align, but 3DLabs
doesn't carry it any more. Do you know which currently available
boards will work with your system?
-
Alas, all the boards that have been tested with IGL Align have now been
discontinued. Hopefully, someone will have the opportunity to try it on
other boards and report back to this FAQ their findings.
In the meantime, I recommend you try using SEM Align instead. SEM Align
works without special purpose hardware.
- Is SEM Align as fast as IGL Align, or would I see a significant performance
advantage with the 3D board and IGL Align?
-
SEM Align is probably not as fast as an Oxygen 402 accelerator
but it is difficult to know a priori whether another accelerator
supports the OpenGL features that would enhance IGL Align's
performance. (This kind of information is just not published by
the manufacturer.)
- In addition to not requiring special purpose hardware,
what other advantages does SEM Align have over IGL Align?
- SEM Align can handle large images (whereas the IGL Align could only
handle images less than the screen size, e.g. 1024x768)
- SEM Align runs on any Win32 operating system (Win95, 98, NT)
- Additional degrees of freedom can be introduced into the alignments
- A point correspondence feature allows automatic alignment based on
a few points input by the user
- Alignment parameters are saved separately from the images so
that alignments can be copied, undone, averaged, and adjusted
IGL Align is a Windows (Win32) application for
aligning serial section images using OpenGL.
This program has been superceded by a more advanced alignment program: sEM Align.