How to make a kymograph?

[Michael Cundell]

Hi,

I recently took a timelapse movie of living cells on a deltavision
microscope that were expressing a fluorescently tagged protein.  I am now
trying to make a kymograph of the timelapse series.  The timelapse
consists of 21 Z-sections per timepoint, with 60 timepoints in total, each
timepoint separated my 30seconds (30minute total timelapse length).  

What i want to do is project the 21 Z's for each timepoint, and then
extend time (ie the 60 timepoints) along a y-axis.  Does anyone know how i
can do this?  

Thanks

Mike

[Michael Cundell]

The kymograph plugin at http://www.embl.de/eamnet/html/kymograph.html is
actually a plugin for measuring velocities from a kymograph rather than
making a kymograph itself.

I guess my question has changed a little.  The main problem I think is
that image J handles my timepoints from my deltavision file in the same
way it handles the stacks.  So basically when i open the file, it doesnt
separate time and stacks.  Therefore when i do a Z-project, it stacks not
only my 21 Z's for each timepoint, but all the subsequent timepoints as
well into a single image.  Ideally it would stack each 21 Z's, but then
allow me to scroll through the timepoints.

Is there a way in image J to stack groups of Z's.  What i really need to i
think is Z-project each 21 Z's but not the timepoints, and then reslice
the resulting image.

[Kota Miura]

Hi Michael,

1. use "Grouped ZProjector" plugin to do the z-projections for each time
point. If the order of dimensions are somehow not matching, then use
"Hypervolume shuffler" plugin before using the above plugin.

2. Then do Image -> Stacks -> Reslice.

Cheers,
Kota



Michael Cundell wrote:

> The kymograph plugin at http://www.embl.de/eamnet/html/kymograph.html is
> actually a plugin for measuring velocities from a kymograph rather than
> making a kymograph itself.
>
> I guess my question has changed a little.  The main problem I think is
> that image J handles my timepoints from my deltavision file in the same
> way it handles the stacks.  So basically when i open the file, it doesnt
> separate time and stacks.  Therefore when i do a Z-project, it stacks not
> only my 21 Z's for each timepoint, but all the subsequent timepoints as
> well into a single image.  Ideally it would stack each 21 Z's, but then
> allow me to scroll through the timepoints.
>
> Is there a way in image J to stack groups of Z's.  What i really need to i
> think is Z-project each 21 Z's but not the timepoints, and then reslice
> the resulting image.
>
>
>  

--
-------------------------------------------------------------
Dr. Kota Miura

Scientist & IT Engineer
Centre for Molecular and Cellular Imaging,
European Molecular Biology Laboratory
Meyerhofstr. 1
69117 Heidelberg
GERMANY

Tel [phone]
Fax [phone]
http://www.embl.org/cmci/
-------------------------------------------------------------

[Wayne Rasband]

On Aug 25, 2008, at 6:13 AM, Kota Miura wrote:

> Hi Michael,
>
> 1. use "Grouped ZProjector" plugin to do the z-projections for each
> time point. If the order of dimensions are somehow not matching, then
> use "Hypervolume shuffler" plugin before using the above plugin.
>
> 2. Then do Image -> Stacks -> Reslice.

The Image>Stacks>Z Project command does "grouped" projections if you
first convert to a hyperstack using the Image>Hyperstacks>Stack to
Hyperstack command. For an example, try doing a Z projection of the
File>Open Samples>Organ of Corti hyperstack (4 channels, 15 slices).

-wayne

>
> Cheers,
> Kota
>
>
>
> Michael Cundell wrote:
>> The kymograph plugin at http://www.embl.de/eamnet/html/kymograph.html 
>> is actually a plugin for measuring velocities from a kymograph rather
>> than making a kymograph itself.
>>
>> I guess my question has changed a little.  The main problem I think
>> is that image J handles my timepoints from my deltavision file in the
>> same way it handles the stacks.  So basically when i open the file,
>> it doesnt separate time and stacks.  Therefore when i do a Z-project,
>> it stacks not only my 21 Z's for each timepoint, but all the
>> subsequent timepoints as well into a single image.  Ideally it would
>> stack each 21 Z's, but then allow me to scroll through the
>> timepoints.
>>
>> Is there a way in image J to stack groups of Z's.  What i really need
>> to i think is Z-project each 21 Z's but not the timepoints, and then
>> reslice the resulting image.
>>
>>
>>
>
> --
> -------------------------------------------------------------
> Dr. Kota Miura
>
> Scientist & IT Engineer
> Centre for Molecular and Cellular Imaging,
> European Molecular Biology Laboratory
> Meyerhofstr. 1
> 69117 Heidelberg
> GERMANY
>
> Tel [phone]
> Fax [phone]
> http://www.embl.org/cmci/
> -------------------------------------------------------------
>