Question: How to do the white-balancing for the RED filter?

Hi: It looks like you are using "Auto" mode when taking the photo. I don't have this camera but I found this web site that might help: https://support.usa.canon.com/kb/index?page=content&id=ART105422&cat=4254B&actp=LIST

You need to follow the instructions for setting a "Custom" white balance except instead of using the white piece of paper use the card that came with the kit. Once the custom white balance is set you need to make sure that the camera's white balance setting is set to "Custom" before taking a photo.

@nedhorning, I'm actually using the "Custom" option following the steps shown here, but using the Red calibration card.

Do the images you acquire using "Auto" mode look the same or very similar to the ones you acquire using the custom white balance?

@nedhorning, actually your question/suggestion fixed the calibration. After switching to "Auto" to take a picture to compare and switching back to "Custom", it seems to have reset the white-balance issue. Now the image looks correct so thank you!

Question: when you do the white-balance process, do you recommend to place the calibration card outside in the shade or directly under the sunlight? Also, when you process images taken with the RED filter, do you use NDVIBlu2RedBW.lut color table in the Fiji Photo Monitoring plugin or is that color table for the BLUE filter?

Nice photos. I suggest using lighting conditions similar to those for the photos you plan to take. Once you get the white balance routine down it's easy enough to do the day you take photos. That said, if you use an old white balance setting with different lighting conditions I wouldn't expect that much of a difference but that would be good to test.

For the color table you can pick one that looks nice. They aren't really designed for the different colored filters since in all cases you are calculating NDVI and in principle NDVI from a red or blue filter should be similar. That's not always the case but they shouldn't be too different. If you want to compare the colored NDVI images with other images that you should use the same color table so they are easy to compare. If you want to show the images to other people it's good to include an insert or legend of the color table so people know how the low and high NDVI values are colored.The Blu2Red in the color table name just means the colors range from blue (low) to red (high).