The following code you sent works well but acquiring ten individual phase-contrast images of the Z plane takes time and slows things down. Thanks again for your patience and support. I'm doing something similar with 'Auto Save' settings, but that does not allow overwriting the files and over time too many phase-contrast images would be accumulated. The exact name of the files is not important for this purpose. Would it be possible to modify the code in order to save the Z stack images as DIC-1, DIC-2, DIC-3.DIC-10 in a specified folder on the computer. Currently, the images are saved as per settings in 'Auto Save' window of Zen. I would like to request one more modification in the code for Query #1. The table was created and displayed, but I get an error- ’table’ is not defined. (Path.GetFileNameWithoutExtension(image.FileName), newfocPos) We are using Zen Blue 2012 and the module for macro environment was added two years back.įor quick reference here’s the revised code you sent for generating the table. I suspect the error is again due to the older version of Zen Blue. However, when running the following code for query # 3, I get the error "NameError: name 'table' is not defined in line 3” The code for Query #2, related to getting the image name from the saved text file, seems to work fine as well. The table is displayed as an untitled window. Now a table is created with the correct image names and corresponding Z positions. The revised code for Query #1 works great. Can you please help with saving the image files names in the table. The Z positions are correct in the table. In this case, all steps work except the name of image files is incorrectly shown in the table as ''. The code worked when line 13 was changed to. I got an error – AttibuteError: 'Zenimage' object has no attribute 'NameWithoutExtenstion' in line 13, when running the following code-Įxperiment = ("DIC.czexp") Thank you very much for your pateince and support. This might be too many questions- but once we have the image file name such as 'DIC-05' available in Zen, would it be possible to access the table generated above (query #1) and access information of the Z position for 'DIC-05' for further single molecule flouresent imaging at the same Z plane as 'DIC-05'. Right now when I open the 'minVar.txt' file, all I see is the name of the image file 'DIC-05' and the question is how to access the 'minVar.txt' from Zen and get the image name 'DIC-05'. From the Zen OAD, is it possible to get the name of the image in 'minVar.txt' file. The Fiji macro saves the name of the Z stack image with the lowest pixel variance in a file named 'minVar.txt'. Image11 = (experiment11)įrom Zen we run a Fiji macro to analyze Z stack images for variance in pixel value. Image10 = (experiment10)Įxperiment11 = ("DIC.czexp") Image9 = (experiment9)Įxperiment10 = ("DIC.czexp") Image8 = (experiment8)Įxperiment9 = ("DIC.czexp") Image7 = (experiment7)Įxperiment8 = ("DIC.czexp") Image6 = (experiment6)Įxperiment7 = ("DIC.czexp") Image5 = (experiment5)Įxperiment6 = ("DIC.czexp") Image4 = (experiment4)Įxperiment5 = ("DIC.czexp") Image3 = (experiment3)Įxperiment4 = ("DIC.czexp") Image2 = (experiment2)Įxperiment3 = ("DIC.czexp") Image1 = (experiment1)Įxperiment2 = ("DIC.czexp") Here's the script we use in Zen for collecting images of the Z stack.įocPos = Įxperiment1 = ("DIC.czexp") While acquiring Z stack images, is it possible to generate a table with image names along with corresponding Z positions? I need help with stringing these steps together for faster image acquisition. Recently we were able to take a series of Z stack images under phase contrast, analyze those images by a Fiji macro, and select the Z plane for single-molecule imaging. So far before doing fluorescent imaging of single molecules, we image cells under phase contrast and manually adjust the focus. We are trying to take advantage of Zen OAD to smoothen the acquisition of single-molecule data from live yeast cells.
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