Search found 14 matches
- Wed Oct 06, 2021 11:19 pm
- Forum: Miscellaneous
- Topic: General Approach to Start an External Application
- Replies: 14
- Views: 8851
Re: General Approach to Start an External Application
Hi, I recently learned about running Fiji from PC's console in Headless mode without opening the program. In my current script, it takes about 11 seconds for Fiji to analyze Z-stack and return results to OAD. I was wondering if OAD supports opening Fiji in Headless mode. Hopefully, Fiji analysis wit...
- Tue Oct 05, 2021 12:15 am
- Forum: Image Acquisition
- Topic: Analyze Z stack images and choose Z plane to image
- Replies: 12
- Views: 4273
Re: Analyze Z stack images and choose Z plane to image
Thanks again for your reply. You correctly anticipated the problem that only checking for the existence of .txt file would not be enough and one has to check if the file can be read. We implemented that, but occasionally the file would show empty content. It seems Zen was reading the .txt file befor...
- Tue Sep 28, 2021 8:02 pm
- Forum: Image Acquisition
- Topic: Analyze Z stack images and choose Z plane to image
- Replies: 12
- Views: 4273
Re: Analyze Z stack images and choose Z plane to image
Sorry, this has become a long chain. I hope it's alright to ask one more question regarding this project. Overall the ZEN OAD script is working great. We generate a Z-stack of phase-contrast images and from within ZEN OAD, we run Fiji macro to analyze plane with the correct focus. Fiji stores the fo...
- Tue Jul 13, 2021 10:38 pm
- Forum: Image Acquisition
- Topic: Analyze Z stack images and choose Z plane to image
- Replies: 12
- Views: 4273
Re: Analyze Z stack images and choose Z plane to image
The Focus Strategy method worked very well. Thank you
- Tue Jul 13, 2021 6:24 am
- Forum: Image Acquisition
- Topic: Analyze Z stack images and choose Z plane to image
- Replies: 12
- Views: 4273
Re: Analyze Z stack images and choose Z plane to image
Hi, thank you for your suggestions and help. The following code you sent works well but acquiring ten individual phase-contrast images of the Z plane takes time and slows things down. ------------------------------------------------------------------------------- from System.IO import Path focPos = ...
- Thu Jul 08, 2021 11:02 pm
- Forum: Image Acquisition
- Topic: Analyze Z stack images and choose Z plane to image
- Replies: 12
- Views: 4273
Re: Analyze Z stack images and choose Z plane to image
Thanks a lot for your help. The revised code for Query #1 works great. Now a table is created with the correct image names and corresponding Z positions. The table is displayed as an untitled window. The code for Query #2, related to getting the image name from the saved text file, seems to work fin...
- Wed Jul 07, 2021 12:15 am
- Forum: Image Acquisition
- Topic: Analyze Z stack images and choose Z plane to image
- Replies: 12
- Views: 4273
Re: Analyze Z stack images and choose Z plane to image
Hi, thank you for your quick response. The codes are super helpful. I got an error – AttibuteError: 'Zenimage' object has no attribute 'NameWithoutExtenstion' in line 13, when running the following code- ------------------------------------------------------------------------------------------------...
- Sat Jul 03, 2021 12:25 am
- Forum: Image Acquisition
- Topic: Analyze Z stack images and choose Z plane to image
- Replies: 12
- Views: 4273
Analyze Z stack images and choose Z plane to image
Hi, We are trying to take advantage of Zen OAD to smoothen the acquisition of single-molecule data from live yeast cells. So far before doing fluorescent imaging of single molecules, we image cells under phase contrast and manually adjust the focus. Recently we were able to take a series of Z stack ...
- Thu Jun 17, 2021 10:27 pm
- Forum: Miscellaneous
- Topic: General Approach to Start an External Application
- Replies: 14
- Views: 8851
Re: General Approach to Start an External Application
The Zen script worked great and the macro in Fiji was called ran very well.
Thank you very much.
Best,
Anand
Thank you very much.
Best,
Anand
- Wed Jun 16, 2021 9:44 pm
- Forum: Miscellaneous
- Topic: General Approach to Start an External Application
- Replies: 14
- Views: 8851
Re: General Approach to Start an External Application
Thank you very much for your quick response. If I understand correctly, you have provided the two different methods for adding information of Fiji macro in the Zen script- ------------------------------------------------------------------------------ def Fiji(macroname, FileOrFolder): ## define Fiji...