Tiled Z stack

[Barbara Smith]

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

We are trying to perform a tiled Z stack on the Zeiss multi-time software.  

We are able to collect multiple Z series, and tiled images in the stage
controller but we have not been able to couple the tile function and 3D
function to form a tiled Z stack.  If anyone has been figured out how to do
a tiled Z stack, any help would be appreciated.  

Thank you,
Barbara

Barbara J. Smith
Microscope Facility Assistant
JHU SOM Microscope Facility
Physiology Building, Room G04
725 N. Wolfe Street, Baltimore, MD 21205
[hidden email]
410-614-6890

[G. Esteban Fernandez]

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Barbara,

 

Is the "ZStackXY" box checked?

 

Here is the (condensed) protocol we use in our lab; let me know if you need more details:

 

1. Set the z boundaries (mark first/last or whatever) and set the gain, offset, etc.

2. Save the configuration.
3. If not already there, focus the 'scope at the first plane in the stack.  This can be accomplished by clicking the "First" button in the Z Settings window.  It is important to do this because by default MultiTime inteprets the present Z location as the first plane in a stack.  This default can be changed to the middle of the stack in the Options, so if the Z stacks are not starting/ending as expected verify this setting.
5. Run the MultiTime macro.

a. Load the configuration where the Z settings, etc. were saved.

b. Select the "ZStackXY" box.

c. Adjust all other parameters as needed and click "Start Time".

 

Good luck!

 

-Esteban

On Fri, Aug 1, 2008 at 1:48 PM, Barbara Smith <[hidden email]> wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

We are trying to perform a tiled Z stack on the Zeiss multi-time software.

We are able to collect multiple Z series, and tiled images in the stage
controller but we have not been able to couple the tile function and 3D
function to form a tiled Z stack.  If anyone has been figured out how to do
a tiled Z stack, any help would be appreciated.

Thank you,
Barbara

Barbara J. Smith
Microscope Facility Assistant
JHU SOM Microscope Facility
Physiology Building, Room G04
725 N. Wolfe Street, Baltimore, MD 21205
[hidden email]
410-614-6890

--
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Core Facility
University of Missouri
120 Bond Life Sciences Center
Columbia, MO 65211

http://www.biotech.missouri.edu/mcc/
573-882-4895

573-884-9395 fax

[Arvydas Matiukas]

Barbara,

 

our facility is sucessfully using MultiTime for years. We are doing similarly as Esteban described. However, few important steps should be added that can be

summarized as step 4.

 

4. a) load the saved configuration from the Multi Time Series Window

    b) Set tiles by Clicking: Edit locations->Tile (set x, y tile number) ->Create tiles

    c) select checkbox to save output tiles as single file

 

The mentioned settings/commands may be slightly different depending on the version of your software.

 

Good luck,

Arvydas

 

 

 

Arvydas Matiukas, Ph.D.
Director of Confocal&Two-Photon Imaging Core Facility
Department of Pharmacology
SUNY Upstate Medical University
766 Irving Ave., WH 3159
Syracuse, NY 13210
tel.: [phone]
fax: [phone]
email: [hidden email]


>>> "G. Esteban Fernandez" <[hidden email]> 8/1/2008 3:38 PM >>>
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Barbara,

 

Is the "ZStackXY" box checked?

 

Here is the (condensed) protocol we use in our lab; let me know if you need more details:

 

1. Set the z boundaries (mark first/last or whatever) and set the gain, offset, etc.

2. Save the configuration.
3. If not already there, focus the 'scope at the first plane in the stack.  This can be accomplished by clicking the "First" button in the Z Settings window.  It is important to do this because by default MultiTime inteprets the present Z location as the first plane in a stack.  This default can be changed to the middle of the stack in the Options, so if the Z stacks are not starting/ending as expected verify this setting.
5. Run the MultiTime macro.

a. Load the configuration where the Z settings, etc. were saved.

b. Select the "ZStackXY" box.

c. Adjust all other parameters as needed and click "Start Time".

 

Good luck!

 

-Esteban

On Fri, Aug 1, 2008 at 1:48 PM, Barbara Smith <[hidden email]> wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

We are trying to perform a tiled Z stack on the Zeiss multi-time software.

We are able to collect multiple Z series, and tiled images in the stage
controller but we have not been able to couple the tile function and 3D
function to form a tiled Z stack.  If anyone has been figured out how to do
a tiled Z stack, any help would be appreciated.

Thank you,
Barbara

Barbara J. Smith
Microscope Facility Assistant
JHU SOM Microscope Facility
Physiology Building, Room G04
725 N. Wolfe Street, Baltimore, MD 21205
[hidden email]
410-614-6890

--
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Core Facility
University of Missouri
120 Bond Life Sciences Center
Columbia, MO 65211

http://www.biotech.missouri.edu/mcc/
573-882-4895

573-884-9395 fax