CZItoTIFFConverter

Your place to discuss general handling of images and the CZI file format
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user-6814
Posts: 7
Joined: Thu Jan 01, 1970 1:00 am

CZItoTIFFConverter

Post by user-6814 »

Good afternoon,
Is there any chance to have the CZItoTIFFBatchConverter software described here? czi files are huge and occupy large parts of the disk. Exporting each czi individually requires a person to do just that and not doing useful things.
Any chance that ZEN would support bigtiff in the near future?
user-4
Posts: 402
Joined: Thu Jan 01, 1970 1:00 am

CZItoTIFFConverter

Post by user-4 »

Hello Ciprian,

here is the download of the CZItoTIFFConverter project.

Please keep in mind that it dates from 2014 and is primarily written for AxioScan (tiles) images.

Therefore 'as is', no guarantee, warranty etc :-)
user-6814
Posts: 7
Joined: Thu Jan 01, 1970 1:00 am

Post by user-6814 »

Thank you!
What about the Bigtiff support in ZEN?
user-4
Posts: 402
Joined: Thu Jan 01, 1970 1:00 am

Post by user-4 »

What about the Bigtiff support in ZEN?
Hello Ciprian,

did you have a look at Menu: File - Export/Import - Export (or alternative: Processing Tab - Image Export - Image Export)?

A window with title Parameters opens and the File Type can be selected as Tiff Format (64 Bit) (BigTiff)
user-6877
Posts: 1
Joined: Thu Jan 01, 1970 1:00 am

Post by user-6877 »

Using ZEN 2.3 lite, I unsuccessfully tried to export a large CZI file (>= 2.4 GB) to an image. No matter whether I chose BigTiff or PNG file format, the resulting file(s) just didn't appear on the disk (although ZEN did some processing for quite a while, as I could see the progress bar).

What might be the reason for such behavior?

PS. Using "CZI to TIFF Batch Converter" I managed to have the job done :)
user-4
Posts: 402
Joined: Thu Jan 01, 1970 1:00 am

Post by user-4 »

With the little information given my guess is that the "CZI to TIFF Batch Converter" is exporting the tiles individually and when using ‘Image Export’ you tried to export the image as a whole. There is a memory 2 Giga restriction within .Net ;-(
Ciprian Popa
Posts: 5
Joined: Thu Apr 22, 2021 3:35 pm

Re: CZItoTIFFConverter

Post by Ciprian Popa »

I see myself constrained to revive this old topic. I recently updated the zen core to v. and the export tool got even worse. No matter of the size (far under a 2 Gb limit) there is no chance to export a czi to tiffs or png's.
CarlZeissMicroscopy3
Posts: 88
Joined: Wed May 20, 2020 10:10 am

Re: CZItoTIFFConverter

Post by CarlZeissMicroscopy3 »

there is no chance to export a czi to tiffs or png's
To consider your case in more detail please let me know which version of Zen Core, including Hotfix, you use, which kind of image (tiled, grayscale, etc.) we talk about and finally how you tried to export the image.

Do you have the 'Open Application Development' (macro-environment) module in your Zen Core application?
Ciprian Popa
Posts: 5
Joined: Thu Apr 22, 2021 3:35 pm

Re: CZItoTIFFConverter

Post by Ciprian Popa »

Hi,
The zencore version is 2.7. In this case the image is a mosaic (hence, presumably tiled) and grey scale. However, the symptoms are the same also with a 3 channel image.
I tried to export it using all the available options in the export menu: e.g. save image, export image as bigtiff, png etc. Tried to reduce the czi image size (https://drive.google.com/file/d/1uNYZMj ... UTRjg/edit) to a manageable one (around 100 Mb) in order to export it. However, every time I try export it it gives the error: "The image is too large and can't be saved in the specified format ()". Please note that the "CZItoTIFFBatchConverter" can handle the file well. However, it cannot preserve information regarding the scale of the image.
CarlZeissMicroscopy3
Posts: 88
Joined: Wed May 20, 2020 10:10 am

Re: CZItoTIFFConverter

Post by CarlZeissMicroscopy3 »

Hello Ciprian Popa,

which Hotfix did you install? Hotfix 7 is now available.

I found the following remarks in the ReadMe:

INCLUDED ARE THE FOLLOWING PROBLEMS FROM HOTFIX 1-7
...
#184302 Images cannot be saved as BigTIFF files
#187700 Save as JPG shows error message "Image is too large"
...

Maybe your case is also covered by the Hotfixes.
Remark: You just need HF7 to cover all the Hotfixes.

I tried to save a huge tiled image with Zen Core 3.1 and it worked for BigTiff (Size = 100%) and JPEG (Size 85%).
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