Import Image-Sequence Bug ?

[microfunguy]

[apologies if double post, the ImageJ server insists on identifying my gmail as googlemail]

Hello,

I need to create eight-bit BMP AVI files and ImageJ is the only programme that I have found so far that can do this.

Unfortunately, there seems to be a bug in the Image import function.

In a sequence of 22 images, the latter 11 become corrupted when converted to a stack.

A 20K file containing the source images is available here  :

http://dl.dropbox.com/u/17639456/ImageJStack.zip


David

[Gabriel Landini]

On Tuesday 07 Feb 2012 18:54:42 [hidden email] wrote:
> I need to create eight-bit BMP AVI files and ImageJ is the only programme
> that I have found so far that can do this.
> In a sequence of 22 images, the latter 11 become corrupted when converted to
> a stack.

Seems to work OK here when I drag the folder into IJ and I select "convert to
RGB".
Cheers
G.

[microfunguy]

> Seems to work OK here when I drag the folder into IJ and I select "convert
> to RGB".


Hi Gabriel.

I have not been on the list for some time, I remember your early work for
stereo support.

I am not converting the images to anything (other than an AVI).

Look at them in the stack and compare with source images.

I am using the very latest ImageJ installed today on Windows XP Pro SP2 with
Java  included.

Here  is the animation which also illustrates how the latter eleven
images appear in the stack :-

http://dl.dropbox.com/u/17639456/waiting.avi

David

[Gabriel Landini]

> I am not converting the images to anything (other than an AVI).
> Look at them in the stack and compare with source images.
> I am using the very latest ImageJ installed today on Windows XP Pro SP2 with
> Java  included.

Hi, Sorry I was not clear. What I meant was that the bmps that you sent, if
loaded as a folder and clicked on Convert to RGB when importing, they will
create the expected stack without the wrong colours.
That is the same as:
run("Image Sequence...", "open=/home/gabriel/Desktop/ImageJStack/ number=22
starting=1 increment=1 scale=100 file=[] or=[] convert_to_rgb sort");

Then saving the stack as AVI (uncompressed) looks OK:

run("AVI... ", "compression=Uncompressed frame=10
save=/home/gabriel/Desktop/ImageJStack.avi");

If I do not click on "Convert to RGB" when importing, I get the corrupted
stack, same as:

run("Image Sequence...", "open=/home/gabriel/Desktop/ImageJStack/ number=22
starting=1 increment=1 scale=100 file=[] or=[] sort");

Not sure why the wrong colours appear.
Was that what you were reporting?

Regards
Gabriel

[microfunguy]

> Not sure why the wrong colours appear.
> Was that what you were reporting?

Yes, but thanks to your information it is not important for my application.

After converting to RGB, I then have to convert back to 256-colour eight-bit
(!) and save as AVI.

That will be a very tiny script that converts BMP files to an AVI suitable
for using as a WIN32 animation control in an AutoIt application.

Many thanks,


David

[Jerome Mutterer-3]

Hi,
The original bmp files were not all saved using the same lookup tables.
When you import the bmp files as a serie, they will all be applied the
first image's loookup table, because 8-bit stacks do not support different
luts for each slice (composite stacks do, however).

Jerome

On 7 February 2012 22:09, <[hidden email]> wrote:

> Not sure why the wrong colours appear.
>> Was that what you were reporting?
>>
>
> Yes, but thanks to your information it is not important for my application.
>
> After converting to RGB, I then have to convert back to 256-colour
> eight-bit (!) and save as AVI.
>
> That will be a very tiny script that converts BMP files to an AVI suitable
> for using as a WIN32 animation control in an AutoIt application.
>
> Many thanks,
>
>
> David

[microfunguy]

Hi,
very interesting.

The first eleven images use ten shades of green, including one almost
completely white.

The second eleven images do not use that shade and the remaining palette
colours are shifted left.


David

[Gabor Csucs]

Dear All,

Perhaps a trivial question but after quite some search I couldn't find a
way to do it, so I turn to the list.

I have a 3D confocal microscope stack (multicolor but this doesn't really
matter). What I'd like to do is to define an arbitrary line in the X-Y
plane and extract an image of my stack that shows the Z information
(image) along my line. With other words: I'd like to make a line profile
but instead of the intensity information I'd like to see the
Z-information/values of my stack. Can anyone pinpoint a
function/plugin/macro which can do this? (I've realized that the "Untilt"
plugin can do something into this direction but it is not exactly what I'd
like to have...

Thanks for the hints Gabor

Light Microscopy and Screening Centre
ETH Zurich, HPM G41
Schafmattstrasse 18
CH-8093, Zurich
Switzerland

Phone: [phone]
Mobile: [phone]

[Cammer, Michael]

Image > Stacks > Reslice [/]...

You may reset slice depth here or reset in Image > Properties...

Here are a few fun things done with this: http://www.flickr.com/search/?q=reslice&w=39998519%40N00&ss=2&s=rec



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Csúcs Gábor
Sent: Wednesday, February 08, 2012 1:48 PM
To: [hidden email]
Subject: Z projection/section along an arbitrary line/plane

Dear All,

Perhaps a trivial question but after quite some search I couldn't find a
way to do it, so I turn to the list.

I have a 3D confocal microscope stack (multicolor but this doesn't really
matter). What I'd like to do is to define an arbitrary line in the X-Y
plane and extract an image of my stack that shows the Z information
(image) along my line. With other words: I'd like to make a line profile
but instead of the intensity information I'd like to see the
Z-information/values of my stack. Can anyone pinpoint a
function/plugin/macro which can do this? (I've realized that the "Untilt"
plugin can do something into this direction but it is not exactly what I'd
like to have...

Thanks for the hints Gabor

Light Microscopy and Screening Centre
ETH Zurich, HPM G41
Schafmattstrasse 18
CH-8093, Zurich
Switzerland

Phone: [phone]
Mobile: [phone]

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

[Olivier Burri]

Hello

The simplest and fastest one is the "Dynamic Reslice" plugin that comes bundled with the Fiji distribution of ImageJ. You can find it here:
http://fiji.sc/wiki/index.php/Dynamic_Reslice

You just have to draw a line and the plugin creates an image as you move the line through your volume. Like Michael said, you should make sure your Z calibration is good.

Best

Oli

Olivier Burri
Engineer, Development in Image Processing
BioImaging and Optics platform (PTBIOP)
Tel: [+4121 69] 39629

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Cammer, Michael [[hidden email]]
Sent: Wednesday, February 08, 2012 8:06 PM
To: [hidden email]
Subject: Re: Z projection/section along an arbitrary line/plane

Image > Stacks > Reslice [/]...

You may reset slice depth here or reset in Image > Properties...

Here are a few fun things done with this: http://www.flickr.com/search/?q=reslice&w=39998519%40N00&ss=2&s=rec



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Csúcs Gábor
Sent: Wednesday, February 08, 2012 1:48 PM
To: [hidden email]
Subject: Z projection/section along an arbitrary line/plane

Dear All,

Perhaps a trivial question but after quite some search I couldn't find a
way to do it, so I turn to the list.

I have a 3D confocal microscope stack (multicolor but this doesn't really
matter). What I'd like to do is to define an arbitrary line in the X-Y
plane and extract an image of my stack that shows the Z information
(image) along my line. With other words: I'd like to make a line profile
but instead of the intensity information I'd like to see the
Z-information/values of my stack. Can anyone pinpoint a
function/plugin/macro which can do this? (I've realized that the "Untilt"
plugin can do something into this direction but it is not exactly what I'd
like to have...

Thanks for the hints    Gabor

Light Microscopy and Screening Centre
ETH Zurich, HPM G41
Schafmattstrasse 18
CH-8093, Zurich
Switzerland

Phone: [phone]
Mobile: [phone]

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================