Koen, These NDVI images look really good. There are multiple reasons that could explain why the trees in the distance have lower NDVI values with the blue-filtered single-camera setup. One very common artifact is caused by scattering of blue light by the atmosphere. Images of distant things look bluer (have higher values for blue) because more blue light coming from all directions gets scattered toward the camera. If you are using the blue channel to represent visible light in calculations of NDVI, higher blue values will compute to lower NDVI values. If you used the red channel to compute NDVI in the two-camera system, red values will not have been inflated by scattering, so that could explain the difference. This Raleigh scattering is one reason to use a red filter instead of blue in single camera systems. Here's an old note about this: http://publiclab.org/notes/cfastie/06-26-2013/infrablue-haze

The 721 nm filter should produce a good pure NIR photo. I'm not sure what the 400 to 700 nm filter will do for you. An unmodified camera gives you that range already. A narrow band red filter might produce a pure red image and better replicate legacy NDVI. But exposure time or aperture will have to compensate for reduced light reaching the sensor.

You might want to try the lut below in Fiji (copy the lut file into the Fiji luts directory). The features of this lut are explained here: http://publiclab.org/notes/cfastie/08-26-2014/new-ndvi-colormap. Feel free to include the jpg below if you post NDVI images made with that lut. .

NDVI_VGYRM.lut

Thanks @cfastie for reminding me of the Raleigh scattering, my equally scattered Sunday evening brain didn't quite put two and two together. The reason for using the 400-700nm filter is to be sure of the range I'm looking at (I know the specs of the filters I use, I don't of the ones that are in the pi cameras). The reason to use this approach instead of just using a single red bandpass is that using the 400-700nm filter will yield me a standard RGB image which is usable in other ways. Mainly I can still use the other channels to calculate a Gcc index (G/R+G+B), using a red bandpass would remove this option. I'm trying to get the most out of the setup (in terms of data streams as well as channels).

I changed the images to your scale. Looks nicer this way. It makes the difference in dynamic range all the more apparent.

Good Job Khufkens I have interest in developing research NDVI using raspberry pi. I still need to learn a little more about it , but I was very enthusiastic about the result.

Sir, did you use any technique or calibration of pinoircamera's white balance?

@khufkens did you set a white balance on the Raspberry Pi for the Infrared image? I use a NoIR V2 camera with the Thorlabs RG9 longpass filter.

The Raspberry Pi v2 camera uses a Sony IMX219 sensor. Here is the spectral response of the sensor found in their datasheet.

RASPBERRY_PI_CAMERA_V2_DATASHEET_IMX219PQH5_7.0.0_Datasheet_XXX.PDF