Search found 14 matches

by Anand Ranjan
Wed Oct 06, 2021 11:19 pm
Forum: Miscellaneous
Topic: General Approach to Start an External Application
Replies: 9
Views: 6194

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...
by Anand Ranjan
Tue Oct 05, 2021 12:15 am
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 471

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...
by Anand Ranjan
Tue Sep 28, 2021 8:02 pm
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 471

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...
by Anand Ranjan
Tue Jul 13, 2021 10:38 pm
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 471

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

The Focus Strategy method worked very well. Thank you
by Anand Ranjan
Tue Jul 13, 2021 6:24 am
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 471

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 = ...
by Anand Ranjan
Thu Jul 08, 2021 11:02 pm
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 471

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...
by Anand Ranjan
Wed Jul 07, 2021 12:15 am
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 471

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- ------------------------------------------------------------------------------------------------...
by Anand Ranjan
Sat Jul 03, 2021 12:25 am
Forum: Image Acquisition
Topic: Analyze Z stack images and choose Z plane to image
Replies: 12
Views: 471

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 ...
by Anand Ranjan
Thu Jun 17, 2021 10:27 pm
Forum: Miscellaneous
Topic: General Approach to Start an External Application
Replies: 9
Views: 6194

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
by Anand Ranjan
Wed Jun 16, 2021 9:44 pm
Forum: Miscellaneous
Topic: General Approach to Start an External Application
Replies: 9
Views: 6194

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...