Analysis in batch mode can only process files in CZI format

Your place to discuss general handling of images and the CZI file format
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Nick Davis
Posts: 8
Joined: Mon Jan 10, 2022 4:16 pm

Analysis in batch mode can only process files in CZI format

Post by Nick Davis »

Hello all,

"Analysis in batch mode can only process files in CZI format"

What am I doing wrong? How am I supposed to conduct image analysis if I only have hundreds of .TIF files?

How can I convert .tif files to CZI?
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Analysis in batch mode can only process files in CZI format

Post by CarlZeissMicroscopy3 »

Hello Nick Davis,

sorry, his is a forum for Open Application Development (OAD).
How am I supposed to conduct image analysis if I only have hundreds of .TIF files?

Code: Select all

## Load measurement program
ias=ZenImageAnalysisSetting()
ias.Load("MyImageAnalysisSetting.czias")

from System.IO import File, Directory, FileInfo

path = "C:\\MyPathToTifFiles"
files = Directory.GetFiles(path,"*.tif")

## loop over all tif-images in the folder

for i in range(0,files.Length):
    file = files[i]
    fileInfo = FileInfo(file)
    PathAndFile = path + "\\" + fileInfo.Name
    image = Zen.Application.LoadImage(PathAndFile,False)

    # The following command has to be activated, if each image should be displayed
    # Zen.Application.Documents.Add(image)

    Zen.Analyzing.Analyze(image,ias)
    ....
I hope this shows in principle how it can be done.
Nick Davis
Posts: 8
Joined: Mon Jan 10, 2022 4:16 pm

Re: Analysis in batch mode can only process files in CZI format

Post by Nick Davis »

As far as open application development, there seems to be plenty of content of going from .CZI to .tiff, and none going from .tiff to CZI.

Why is file converting the other way not considered “open application development?” And I have the latest Zen software.
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Analysis in batch mode can only process files in CZI format

Post by CarlZeissMicroscopy3 »

Why is file converting the other way (.tiff to .CZI) not considered in “open application development?”
Hello Nick Davis,

The answer is simple: There is no conversion needed for tif, just load it!

Code: Select all

zenImage = ZenImage()
PathAndFile = "C:\\MyPath\\MyImage.tif"
zenImage.Load(PathAndFile)

# if you want to see it ;-)
Zen.Application.Documents.Add(zenImage)
compare it to czi

Code: Select all

zenImage = ZenImage()
PathAndFile = "C:\\MyPath\\MyImage.czi"
zenImage.Load(PathAndFile)

# if you want to see it ;-)
Zen.Application.Documents.Add(zenImage)
There is no difference!
Mariah Carey
Posts: 1
Joined: Mon May 29, 2023 9:00 am

Re: Analysis in batch mode can only process files in CZI format

Post by Mariah Carey »

Both Bio-Formats and Fiji/ImageJ provide a user-friendly interface and support batch processing, which means you can convert multiple .tif files to CZI at once. mapquest directions
Rose J Lever
Posts: 23
Joined: Tue Jun 20, 2023 10:20 pm

Re: Analysis in batch mode can only process files in CZI format

Post by Rose J Lever »

The CZI file format is a proprietary format developed by Carl Zeiss Microscopy. It is commonly used in the field of microscopy to store multidimensional image data, including information about channels, time points, and image metadata. CZI files can contain both 2D and 3D image data, making them suitable for a wide range of microscopy applications.

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