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multiple channels rgb file

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Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

multiple channels rgb file

Postby michaelgoelzer » Thu Oct 20, 2016 2:19 pm

I tried importing an image with multiple RGB channels (4 RGB channels, 12 channels total) using the Bioformats Plugin for ImageJ.

While the import did work in principle, I could not maintain the RGB-ness in any sensible way.
The best I could do was to import the image with activated "Split channels" option and subsequently merging pairs of 3 into composite images using ImageJ's "Image->Color -> Merge channels..." functionality. However that is quite cumbersome as it is not straightforward to determine which channels are which color after they are imported as grayscale.

The Log says "Warning: Data has too many channels for Colorized color"
(for example, exact words depend on which color mode is chosen)

As for my FormatReader:
- isRGB() returns true
- getRGBChannelCount() returns 3
Both of which seem to make sense. I don't know what other functions are relevant.

Is this case generally not supported, or is there an issue with my FormatReader?
michaelgoelzer
 
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Joined: Wed Oct 19, 2016 9:34 am

Re: multiple channels rgb file

Postby bramalingam » Fri Oct 21, 2016 4:26 pm

Hi,

Thank you for submitting your issue.

This is a known limitation of ImageJ ("Composite" mode will only work with up to 7 channels).

As a workaround, you could open with:
"Split Channels" and "Composite" mode selected in the "Bio-Formats Import Options" window, while importing the image.

You can import 3/6 channels at a time in the composite mode, to view 1/2 RGB images at a time.
Please let us know if this does not work.

macro example:
Code: Select all
run("Bio-Formats Importer", "open=/PATH/TO/RGB/IMAGE color_mode=Composite rois_import=[ROI manager] split_channels view=Hyperstack stack_order=XYCZT");


Hope that helps.
Best,
Balaji
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bramalingam
 
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