CZI to SUR (Topo)

Your place to discuss general handling of images and the CZI file format
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user-6850
Posts: 18
Joined: Thu Jan 01, 1970 1:00 am

CZI to SUR (Topo)

Post by user-6850 »

Hello.

I am using ZEN Blue 2.6 and getting z stack images.
I am also analyzing the height information using the ConfoMap app from the "Applications" tab.
Please tell us about the following two.

1. Is it possible to convert ".czi" file to ".sur" (Topo) by using ZEN macro?

2. Is it possible to control ConfoMap application by using ZEN macro?

Thank you.
user-4
Posts: 398
Joined: Thu Jan 01, 1970 1:00 am

Post by user-4 »

Hello Yosuke,

from your short description I assume you use ZEN Blue 2.6 with an LSM system to acquire the z-stacks.

Is it possible to convert ".czi" file to ".sur" (Topo) by using ZEN macro?

Here is a code snippet to convert a confocal z-stack into a topo image plus saving it to a SUR file:

Code: Select all


imgtop = Zen.Processing.Transformation.Topography.CreateTopography(imgzstack, 1, 254) #0, 255 means no filter, for 8 bit images
# saving file to the directory
Zen.Processing.Utilities.ExportHeightmapFromTopography(fullpath+".sur")


Is it possible to control ConfoMap application by using ZEN macro?

To control ConfoMap its own API needs to be used. There are some different ways to do it.
Probably the simplest one: file with commands. See the SDK.chm file.

For example the mountains.log ASCII file can consist of the following commands:

Code: Select all

HIDE
MESSAGES OFF
AUTOSAVE OFF
NEW_DOCUMENT
LOAD_DOCUMENT "D:\USERS\Test\LSM_Demo_project\_results\final_stats.mnst"
SHOW
Clearly, this file can be created and written from OAD.

Please contact the ConfoMap Support etc. to get further information concerning the API(s)!
The code obove is just a hint!
user-6850
Posts: 18
Joined: Thu Jan 01, 1970 1:00 am

Post by user-6850 »

Hello.

Thank you for your reply.

I was able to get a SUR file.

Thank you for very good advice!
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