"MultichannelMode" and "PixelType" in some InitializeSetting methods

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user-4723
Posts: 8
Joined: Thu Jan 01, 1970 1:00 am

"MultichannelMode" and "PixelType" in some InitializeSetting methods

Post by user-4723 »

Hi ZEN scripting fellows,

This is continuation of the exchange from my previous posts on OAD metadata, which I am initiating a new one to make the issue more accessible.

I noticed that when initializing in ZEN2 the processing settings for (Utilities.)ExportSingleFile by using InitializeSettingForExportSingleFile method, acting on 12bit gray-scale czi image stacks, after scene splitting and stitching+fusing, within the initial XML settings file
- "MultichannelMode" property gets defaulted to "ChannelComposite" without menu item in the parameters dialog explicitly tackling multiple image channels,
- "PixelType" is not present in the initial XML schema,
- output of the "ExportSingleFile" after selecting TIFF format, creates RGB 24bit images for each Z-slice, which is not the typical output if you start with 12Bit gray-scale.
Checking the full metadata generated with the export I found correct, i.e. expected parameters, 16bit gray-scale, single channel.

Saving a single slice from the .czi stack vie "SaveAs" in main ZEN menu, was again creating 24bit composite files, with PixelType = Bgr24 in the basic .xml info file.

When I checked the related export ExportOmeTiff again via InitializeSetting, I realized that it is using MultichannelMode = DistinctChannels, which applied to the same feature within ExportSingleFile changed the behavior, generating 16bit gray-scale, single channel. The XML file of the later method was also having some extra parameters, common for both exports which the former was missing like ConvertTo8bit.

Will appreciate your comment what might be causing this variations, and is there something like a common extended list of parameters for export utility methods.

Regards, Predrag
user-6
Posts: 382
Joined: Thu Jan 01, 1970 1:00 am

Post by user-6 »

Dear Predrag,

we've forwarded your inquiry to our responsible specialist for file export.
We will look into this in more details and try to provide you with an answer
beginning of next week. Thanks for understanding!
user-9
Posts: 82
Joined: Thu Jan 01, 1970 1:00 am

Post by user-9 »

ExportSingleFile acting on 12bit gray-scale czi image stacks,...
- "MultichannelMode" property gets defaulted to "ChannelComposite"
- "PixelType" is not present in the initial XML schema,
- output of the "ExportSingleFile" after selecting TIFF format, creates RGB 24bit images for each Z-slice, which is not the typical output if you start with 12Bit gray-scale.
Checking the full metadata generated with the export I found correct, i.e. expected parameters, 16bit gray-scale, single channel.
Saving a single slice from the .czi stack vie "SaveAs" in main ZEN menu, was again creating 24bit composite files, with PixelType = Bgr24 in the basic .xml info file.
...ExportOmeTiff[/I] ... is using MultichannelMode = DistinctChannels, which applied to the same feature within ExportSingleFile changed the behavior, generating 16bit gray-scale, single channel. The XML file of the later method was also having some extra parameters, common for both exports which the former was missing like ConvertTo8bit.
Export functions show the same behaviour in ZEN meu as in OAD macro
Exported TIFF images have 16-bit for Original data and 24-bit RGB for individual channel and merged channel images
Apply Display curve and Channel Color always generates 24-bit RGB images.
Pixel type is present in …meta.XML.

OME TIFF Export with Original data generates 16-bit pseudo color image.
Apply Display Curve and Channel Color always generates 24-bit image.
OME TIFF can read exported image as is. Therefore OME TIFF Export has no Convert to 8 -bit option.
Save As (tiff) in the ZEN menu generates 8-bit BW images. Pixel information is not present in XML-file.
davis john
Posts: 1
Joined: Thu Mar 30, 2023 10:53 am

Re: "MultichannelMode" and "PixelType" in some InitializeSetting methods

Post by davis john »

Regarding your question about a common extended list of Snow Rider 3D parameters for export utility methods, I'm not aware of a comprehensive list that covers all possible parameters. However, the ZEN scripting documentation does provide information on the available parameters for each method, and how to use them. You may also find it helpful to review the ZEN user manual or contact the ZEN support team for assistance.
orbor neee
Posts: 2
Joined: Thu Jul 20, 2023 3:18 am

Re: "MultichannelMode" and "PixelType" in some InitializeSetting methods

Post by orbor neee »

i'm also looking for data on this extended parameter list, they almost don't appear in any news site! Super Mario
quitzo nsand
Posts: 6
Joined: Mon Apr 03, 2023 10:08 am

Re: "MultichannelMode" and "PixelType" in some InitializeSetting methods

Post by quitzo nsand »

I, too, would like to get some information about the aforementioned supplementary parameters, as they seem to never make the headlines. geometry dash
Quinn Hank.2
Posts: 1
Joined: Wed Aug 23, 2023 5:00 pm

Re: "MultichannelMode" and "PixelType" in some InitializeSetting methods

Post by Quinn Hank.2 »

Continuing the discussion from my earlier posts on OAD metadata, I'm creating a new thread to make the issue more accessible. I've been exploring the behavior of initializing processing settings for (Utilities.)ExportSingleFile using the InitializeSettingForExportSingleFile method in ZEN2. Specifically, I'm working with electrical estimating 12-bit grayscale CZI image stacks and noticed some peculiarities after scene splitting, stitching, and fusing.
Asif Naveed
Posts: 6
Joined: Thu Aug 03, 2023 10:29 pm

Re: "MultichannelMode" and "PixelType" in some InitializeSetting methods

Post by Asif Naveed »

I'm not sure which language or software you're using, but if it were something like Python, you could likely use a library like PyTiff to pull out this information from the metadata. From there FilmPlus MOD APK, you could use that Z-value as your starting point for autofocus.
Antonio Kevin
Posts: 1
Joined: Thu Nov 02, 2023 9:21 pm

Re: "MultichannelMode" and "PixelType" in some InitializeSetting methods

Post by Antonio Kevin »

You should carefully review and customize the export settings within the software, explicitly specifying the desired pixel type (e.g., 16-bit grayscale) and output format (e.g., TIFF) to ensure it matches your expectations. You may want to consult the software's documentation or reach out to their support team for more specific guidance on how to adjust these settings effectively and obtain the desired output when working with CZI image stacks.
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