Multidimensional images

[Gareth Howell]

Dear list
I have a series of 16-bit tiff images from a timecourse experiment. They are two colour and at each time point 10 images were collected in z.
What is the best plugin to use for this type of data to produce an MIP of the two colours over the timecourse and export as an AVI?
Thanks
Gareth

[John Oreopoulos]

Gareth,

I would convert your images into a hyperstack (a standard ImageJ  
feature now, not a special plugin), merge the two color channels and  
do a MIP/z-project. You will be able to scroll through the MIP in  
time with both colors present. Just be sure to select the right order  
of images for the hyperstack (xyzct, xyztc, etc.). I've heard that  
the plugin Image5D is also good for this kind of thing but I haven't  
used it.

John Oreopoulos


On 18-Nov-09, at 6:12 AM, Gareth Howell wrote:

> Dear list
> I have a series of 16-bit tiff images from a timecourse experiment.  
> They are two colour and at each time point 10 images were collected  
> in z.
> What is the best plugin to use for this type of data to produce an  
> MIP of the two colours over the timecourse and export as an AVI?
> Thanks
> Gareth

[Wayne Rasband]

 > Dear list I have a series of 16-bit tiff images from a
 > timecourse experiment. They are two colour and at each time
 > point 10 images were collected in z. What is the best plugin
 > to use for this type of data to produce an MIP of the two
 > colours over the timecourse and export as an AVI?
 > Thanks
 > Gareth

This can be done without a plugin.

1. Open the series as a stack
2. Convert to a hyperstack using Image>Hyperstacks>Stack to Hyperstack
3. Use Image>Stacks>Z Project to produce the MIP
4. Convert to RGB using Image>Type>RGB Color
5. Export as AVI using File>Save As>AVI

-wayne