data.
Please let me know how it works for you.
Post by Christine LabnoHi Curtis,
No worries about the delay, we can get the results we need with either
hyperstack functions or image calculator.
I only get the error with stacks of >3 color channels. The fly brain
red/green RGB stack or the neurons 5 channel / 2D image both work just fine
for me too.
The only sample image I can use to reproduce the error is the Organ of
Corti sample converted from hyperstack to stack. Unfortunately there isn't
much change over the volume so it doesn't make for a very dramatic example.
If you pull through the result quickly all looks OK, but compare the three
spheres in the upper righthand corner of the object frame by frame.
For added fun, before you run Image5D Stack to RGB, set the Image5D display
to the last channel (or any channel other than 1). This frame will always
be the first frame of the resulting RGB stack. The next frame should be
frame 1, or half of frame 15 and half frame 1. Again this only happens with
stacks of >4 color channels.
I can get the fly brain sample to produce the error, but only if I do
something really contrived: Open it, split the color channels so you have
three stacks (blue is empty). Duplicate all z-planes of both the red and
the green stacks. Concatenate green, red, green-1 and red-1 to make, in
essence, a 4 color channel z-stack with 3rd dim = z (57) and 4th dim = c
(4). There is more change over z here, so the effect of the bug is more
dramatic.
If you email me your FTP off list, I'll upload one of our test .tiff stacks
and/or the Slidebook files they were exported from. With those there is no
doubt something is not right.
---- Original message ----
Date: Fri, 3 Dec 2010 14:36:25 -0600
Subject: Re: Image5D Stack to RGB (old z-stack bug?)
Hi Christine,
Really sorry for the long delay in my reply.
I'm trying to create 4 color z-stacks with Image5D using the Image5D Stack
Post by Christine Labnoto RGB feature. When I have a 2D image (one z plane) output is fine,
but
Post by Christine Labnowhen I have multiple z-planes the output is scrambled. Whichever slice
is
Post by Christine Labnodisplayed when I choose "Image5D Stack to RGB" is the first in the
resulting
Post by Christine Labnoz-stack, and parts of some stacks are mixed with others, so the top half
of
Post by Christine Labnothe image will change, but not the bottom.
Unfortunately, in my brief testing I was unable to duplicate the issue
(ImageJ 1.44j, OS X 10.6.5, Image5D 1.2.1).
First I opened a sample RGB Z-series using File > Open Samples > Fly
Brain.
Then I converted it to Image5D using Plugins > Image5D > RGB to Image5D,
accepting the default values, which were correct. The resultant Image5D
window displayed the data correctly. I was then able to create a new RGB
image stack using Plugins > Image5D > Image5D Stack to RGB, which looked
identical to the image planes displayed in the Image5D window.
What am I doing wrong? I would be happy to send a sample stack if that
Post by Christine Labnowould be helpful. Thanks!
Are you able to duplicate the error with any of the sample datasets
available from the Open Samples menu? If so, can you describe the steps
that
produce the problem? If the problem is only with one of your datasets, let
me know and I can provide you with a server for uploading the data.
Thanks,
Curtis
On Thu, Nov 18, 2010 at 12:32 PM, Christine Labno <
Post by Christine LabnoHello all,
I'm trying to create 4 color z-stacks with Image5D using the Image5D
Stack
Post by Christine Labnoto RGB feature. When I have a 2D image (one z plane) output is fine,
but
Post by Christine Labnowhen I have multiple z-planes the output is scrambled. Whichever slice
is
Post by Christine Labnodisplayed when I choose "Image5D Stack to RGB" is the first in the
resulting
Post by Christine Labnoz-stack, and parts of some stacks are mixed with others, so the top half
of
Post by Christine Labnothe image will change, but not the bottom.
This bug was reported in Oct 2009, but I didn't see a clear solution
posted
Post by Christine Labnoother than the Image5D 1.2.1 build released by Joachim Walter. I tried
this, and it fixed the extra, non-functional z-scroll bar, but not the
scrambled RGB Z-stack output.
Systems: ImageJ 1.44i or Fiji with Windows XP 32-bit or Windows 7 32-bit
or
Post by Christine Labno64-bit -- all using either Image5D or the new Image5D 1.2.1.
What am I doing wrong? I would be happy to send a sample stack if that
would be helpful. Thanks!
Christine