Search found 83 matches

by CarlZeissMicroscopy3
Thu Oct 28, 2021 5:10 pm
Forum: Image Processing
Topic: CZI to Tiff64 s z c splitted
Replies: 3
Views: 8

Re: CZI to Tiff64 s z c splitted

Hello Lug Maxwell, I organized some similar images but when trying your export settings individual images for each s z c combination appeared, just as reported. Opening these files just show images ‘as expected’ … But there are two questions on my side: Which hotfix for Zen 3.1 did you install. Hotf...
by CarlZeissMicroscopy3
Wed Oct 27, 2021 12:04 pm
Forum: Image Processing
Topic: CZI to Tiff64 s z c splitted
Replies: 3
Views: 8

Re: CZI to Tiff64 s z c splitted

Hello Lug Maxwell,

just to get some further information:

Your CZI file consists of 4 scenes with z=5 and 3 fluorescent channels.

When we consider just one plane of a scene (e.g. scene 1, z-stack-plane 1, channel 1) is this a tiled image or a single image?
by CarlZeissMicroscopy3
Wed Oct 20, 2021 10:04 am
Forum: Image Processing
Topic: Issue opening a .czmodel in python
Replies: 3
Views: 46

Re: Issue opening a .czmodel in python

Can the trained Intellesis models be run outside of the Zen ecosystem?
Sorry no, not with current releases.

But this is of course a feature to be discussed for future Zen versions.

Thank you for your contribution!
by CarlZeissMicroscopy3
Tue Oct 19, 2021 12:52 pm
Forum: Image Processing
Topic: Issue opening a .czmodel in python
Replies: 3
Views: 46

Re: Issue opening a .czmodel in python

Hello Elizabeth Pereira, Files exported from the Zeiss Intellesis module (wizard, trained etc.) are not ONNX compatible. In Open Application Development (OAD) of Zen there is an object model which can be accessed via macro (Iron-Python). The root object is ZenIntellesis and features are like: ZenInt...
by CarlZeissMicroscopy3
Mon Oct 18, 2021 1:53 pm
Forum: ZEN Core Specific Topics
Topic: Apply macro on selected images in Output area
Replies: 2
Views: 106

Re: Apply macro on selected images in Output area

Hello Fredrik Olsson, starting with Zen Core 3.4 the command Zen.Application.GetFreeModeSelectedOutputParameters() will be available. So the following lines of code will handle all selected images: selectedOutputParameters = Zen.Application.GetFreeModeSelectedOutputParameters() print OutputParameter...
by CarlZeissMicroscopy3
Thu Oct 07, 2021 9:52 am
Forum: Miscellaneous
Topic: General Approach to Start an External Application
Replies: 9
Views: 6271

Re: General Approach to Start an External Application

Hello Anand Ranjan, I was wondering if OAD supports opening Fiji in Headless mode. Please keep in mind that with import clr from System.Diagnostics import Process app = Process(); you import a library from the .Net Framework in OAD and therefore no direct 'OAD support opening Fiji' exists. So, if yo...
by CarlZeissMicroscopy3
Tue Oct 05, 2021 9:15 am
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 606

Re: Analyze Z stack images and choose Z plane to image

Hello Anand Ranjan,

thank you for posting your final solution!

Although the empty file might be a peculiarity of Fiji other people can profit from your experience.
by CarlZeissMicroscopy3
Thu Sep 30, 2021 10:21 am
Forum: Miscellaneous
Topic: Install opencv-contrib
Replies: 6
Views: 330

Re: Install opencv-contrib

Hello Matthew Cottrell, thank you very much for your contribution! This is apparently one way to go. By using import win32com.client Zen = win32com.client.GetActiveObject("Zeiss.Micro.Scripting.ZenWrapperLM") it must be clear that this is just for Zen blue and cannot be used in case of Zen...
by CarlZeissMicroscopy3
Wed Sep 29, 2021 11:27 am
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 606

Re: Analyze Z stack images and choose Z plane to image

Hello Anand Ranjan, happy to hear that your OAD macro works great. File.Exists(path) is not an OAD command. This is one of the strengths of OAD that you can import .Net DLLs e.g., from the .Net Framework, and use them! You get class File by importing from System.IO at the beginning of your code. In ...
by CarlZeissMicroscopy3
Mon Sep 27, 2021 11:44 am
Forum: Image Acquisition
Topic: ZEN multiple Z stack acquisitions
Replies: 1
Views: 59

Re: ZEN multiple Z stack acquisitions

Hello J Seeler, from my understanding you want to fix your z-Stack with the first (bottom) slice. Did you try the Offset in the Center tab. This can shift the ‘center’ to the ‘first’ slice. Something like Offset 15 and Interval 3, Slices 11 (Range 30) Maybe the ‘Show all’ on the right-hand side of t...