Micro-Manager

kinetic series

Classic

List

Threaded

4 messages Options

fiverman

kinetic series

Hi All

I am using Andor Ixon X3 and Nikon Eclipse Ti motorized microscope. I would like to take a movie (kinetic series) at specified xy positions (I have a list of xy positions). It does not seem MM supports this? What I could do is take a series of individual images at every xy position and later manually combine them to a stack. When doing so the software fails to automaticaly save all of the images (lack of mamory?). Is there any way around this problem? Thank you for your help.

Jernej

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

Remove Ads

Nico Stuurman-4

Re: kinetic series

I am using Andor Ixon X3 and Nikon Eclipse Ti motorized microscope. I would like to take a movie (kinetic series) at specified xy positions (I have a list of xy positions). It does not seem MM supports this?

It does.

What I could do is take a series of individual images at every xy position and later manually combine them to a stack. When doing so the software fails to automaticaly save all of the images (lack of mamory?). Is there any way around this problem? Thank you for your help.

I am not sure what you are doing. However, in the Multi-Dimensional Acquisition Windows, check "Time points", set the desired number and Interval to 0, check "Multiple positions (XY)" and select the positions that you are interested in, for Acquisition order, check "Position, Time" and press Acquire.

B.t.w. doing this using the demo equipment suggests that there is a bug in this method in the acquisition window. If you encounter this, please report.

Best,

Nico

fiverman

Re: kinetic series

Thank you Nico for your time. Just to be sure you know what I mean - I would like to take a movie at the specific xy positions. In Andor Solis software this is called Acquisition mode, where you choose kinetic.
I can not find this option in MM. I can take an individual image or a series of images, which will be saved as individual files. I would like to have one tif file at every xy position (a stack of images). I was also looking at the Property Browser under Tools menu in MM. There is only AndorOptAcquireMode menu, but no kinetic series option.
http://www.2shared.com/uploadComplete.jsp?sId=Tu5DuVxZwL5ydIWe

What am I missing?

Nico Stuurman

Re: kinetic series

Administrator

Hello fiverman,

> Just to be sure you know what I mean - I would like to take a movie at the specific xy positions. In Andor Solis software this is called /Acquisition mode/, where you choose /kinetic/. I can not find this option in MM. I can take an individual image or a series of images, which will be saved as individual files.

There you go. Same things as what Solis calls "kinetic series" (or whatever).

> I would like to have one tif file at every xy position (a stack of images).

Although this is on the ToDo list, Micro-Manager still have no native support for multi-page TIFF files. However, acquire your dataset as I described previously, then save from the ImageJ menu (for each individual position). That should save the dataset into a single file as you desire. Repeat the save procedure for each of the positions (lowest slider in the data window).

> I was also looking at the /Property Brow/ser under /Tools/ menu in MM. There is only /AndorOptAcquireMode/ menu, but no /kinetic series /option.

Again, use Micro-Manager's Multi-Dimensional Acquisition.

Best,

Nico

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general