Open Microscopy Environment

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?

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