FV 500 XYZT reconstructions

[js1719]

I have a grad student who is using a FV 500 confocal and taking 2 channel XYZT scans of fibroblasts on synthetic fibers. She wishes to render them to play collectively  like a movie.  I know how to use the 3-D visualize for single z stacks but am not sure how to do it with multiple z stacks over time. If you are a Olympus FloView user could you perhaps contact me to let me know how I might do this? Also, if you know of how to do this in Image J or another offline analysis program please let me know as well. 

thanks 

Julia Sable

Julia E. Sable

Research Associate/ Lab Manager

Sheetz Lab

Columbia University

Dept. of Biological Sciences

[phone]

[hidden email]

[mmodel]

Answer by Rob Clements:

 

“In imagej you have to render a single 3d frame per time stack, and then concatenate each image together.  Or, render  3d-visualizations  for each timepoint and then split it into individual frames and recombine them.  For example, if you have  4 timepoints (a,b,c,d) and render 4 3-d visualiziation frames per stack (a1,a2,a3,a4,b1,b2,b3....) save each stack as an image series and then place the first frame of each in a directory (a1,b1,c1,d1...) and the second in another directory (a2,b2,c2,d2) and so on.  Then, load each of the new stacks and concatenate all the stacks together to create the final movie.” 

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of js1719
Sent: Wednesday, March 04, 2009 3:30 PM
To: [hidden email]
Subject: FV 500 XYZT reconstructions

 

I have a grad student who is using a FV 500 confocal and taking 2 channel XYZT scans of fibroblasts on synthetic fibers. She wishes to render them to play collectively  like a movie.  I know how to use the 3-D visualize for single z stacks but am not sure how to do it with multiple z stacks over time. If you are a Olympus FloView user could you perhaps contact me to let me know how I might do this? Also, if you know of how to do this in Image J or another offline analysis program please let me know as well. 

thanks 

Julia Sable

 

 

 

 

Julia E. Sable

Research Associate/ Lab Manager

Sheetz Lab

Columbia University

Dept. of Biological Sciences

[phone]

[hidden email]

 

 

[js1719]

thanks so much! I forgot about concatenate in Image J

On Mar 5, 2009, at 9:56 AM, MODEL, MICHAEL wrote:

Answer by Rob Clements:

 

“In imagej you have to render a single 3d frame per time stack, and then concatenate each image together.  Or, render  3d-visualizations  for each timepoint and then split it into individual frames and recombine them.  For example, if you have  4 timepoints (a,b,c,d) and render 4 3-d visualiziation frames per stack (a1,a2,a3,a4,b1,b2,b3....) save each stack as an image series and then place the first frame of each in a directory (a1,b1,c1,d1...) and the second in another directory (a2,b2,c2,d2) and so on.  Then, load each of the new stacks and concatenate all the stacks together to create the final movie.” 

 

From: Confocal Microscopy List [[hidden email]] On Behalf Of js1719
Sent: Wednesday, March 04, 2009 3:30 PM
To: [hidden email]
Subject: FV 500 XYZT reconstructions

 

I have a grad student who is using a FV 500 confocal and taking 2 channel XYZT scans of fibroblasts on synthetic fibers. She wishes to render them to play collectively  like a movie.  I know how to use the 3-D visualize for single z stacks but am not sure how to do it with multiple z stacks over time. If you are a Olympus FloView user could you perhaps contact me to let me know how I might do this? Also, if you know of how to do this in Image J or another offline analysis program please let me know as well. 

thanks 

Julia Sable

 

 

 

 

Julia E. Sable

Research Associate/ Lab Manager

Sheetz Lab

Columbia University

Dept. of Biological Sciences

[phone]

[hidden email]

 

 

[Andreas Bruckbauer]

Hi,
when working with XYZT data sets in imagej  the bioformats plugin
http://www.loci.wisc.edu/ome/formats.html and image5D
http://rsb.info.nih.gov/ij/plugins/image5d.html  are most useful for opening
the files (including Olympus oib) and looking through z and t and the
channels, but might not be useful for 3d reconstructions. Imaris does this
quite well...

Andreas

[Vincent Schoonderwoert]

Hi Julia,    (Commercial Interest)

The freeware capabilities of our Huygens Essential software allows you to convert images between different space and time dimensionality's. Under "Tools" you find for example "Convert XYZ to XYZT". The software will only ask for the z dimension (number of z planes).  See also this Wiki page on Tiff series.
You can download the freeware Huygens version from our website: www.svi.nl

Best, Vincent


719 wrote:

thanks so much! I forgot about concatenate in Image J

On Mar 5, 2009, at 9:56 AM, MODEL, MICHAEL wrote:

Answer by Rob Clements:

 

“In imagej you have to render a single 3d frame per time stack, and then concatenate each image together.  Or, render  3d-visualizations  for each timepoint and then split it into individual frames and recombine them.  For example, if you have  4 timepoints (a,b,c,d) and render 4 3-d visualiziation frames per stack (a1,a2,a3,a4,b1,b2,b3....) save each stack as an image series and then place the first frame of each in a directory (a1,b1,c1,d1...) and the second in another directory (a2,b2,c2,d2) and so on.  Then, load each of the new stacks and concatenate all the stacks together to create the final movie.” 

 

From: Confocal Microscopy List [[hidden email]] On Behalf Of js1719
Sent: Wednesday, March 04, 2009 3:30 PM
To: [hidden email]
Subject: FV 500 XYZT reconstructions

 

I have a grad student who is using a FV 500 confocal and taking 2 channel XYZT scans of fibroblasts on synthetic fibers. She wishes to render them to play collectively  like a movie.  I know how to use the 3-D visualize for single z stacks but am not sure how to do it with multiple z stacks over time. If you are a Olympus FloView user could you perhaps contact me to let me know how I might do this? Also, if you know of how to do this in Image J or another offline analysis program please let me know as well. 

thanks 

Julia Sable

 

 

 

 

Julia E. Sable

Research Associate/ Lab Manager

Sheetz Lab

Columbia University

Dept. of Biological Sciences

[phone]

[hidden email]