Merging multispectral projects in Pix4Dmapper

Instructions for merging multispectral projects or merging a multispectral project with an RGB project so that the reflectance maps align with the RGB orthomosaic.

Marking MTPs in multispectral project

The full workflow for merging projects in Pix4Dmapper is described in How to merge projects article.

However, the difference for a multispectral project is that the MTPs need to be marked in each band for each image, e.g. if the MTP1 is marked in an image of the Green band, it will also have to be marked in the Red, Red edge and NIR images that correspond. Hence, what would be one mark in an RGB project results in four marks in a multispectral project (if there are four bands). In addition, you have to mark your MTP in at least three sets of images. Therefore, there should be at least twelve (3*4marks) for each MTP in the project.

Once all MTPs are added, click Menu Process > Reoptimize to apply the changes.  

Use of radiometric targets in merged projects

Pix4D supports only one set of radiometric calibration target images.

In order to get merged reflectance maps, we recommend unselecting duplicate parameters as mentioned in Step 8 of the How to merge projects article.

Important: If duplicate parameters option is selected, multiple radiometric targets can be used, however, the reflectance maps will not be merged. For example, when merging two Micasense projects with five bands, ten reflectance maps will be generated. Hence this procedure would not be of your interest because you will get no extra benefit compared with processing projects individually. 
Note: If you have two flights, we recommend using the target images that were captured after the first flight and before the second flight.
However, if the weather condition between those flights were different, we suggest processing the projects separately and then merging the reflectance maps in QGIS/ArcMap.
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  • Isabell Eischeid

    I am struggling with joining to multispectral projects (had a battery changed that caused that): I have flown with the eBeeX, so I don't have GCPs but accurate enough infornation from using a dGPS base inflight. There are no distinct features so setting manual tie points has not worked. So I tried: 1) Just click merge ignoring that I don't have tie points but when I click the -next- button nothing happens (it's not frozen, I can click back and that works fine). Alternatively, I though I could 2) merge all the images into one folder but I used a Sequoia+ need the therm.dat file in the same folder and I assume that changing the name of one of them would make it not readable/or the proggram would get confused with two therm.dat files.

    So what is the best way of proceeding?


  • Momtanu (Pix4D)

    Isabell if you don't have any specific features for marking, you can process both the projects and then merge the outputs in QGIS. Let me know how it goes.

  • Isabell Eischeid

    Sounds good! Thanks for the quick reply!!!

  • Isabell Eischeid

    The section where both reflectance maps are overlapping have very different values (not just at the edges). That makes me not so safe about using the camera internal calibration. I saw that the therm.dat files for both subprojects have exactly the same size. Is it maybe the same? (both sets are the same mission with a battery change-so they became two folders in emotion). Is there any way to look at the content of these dat files? Or is there a possibilty to merge them? I ran the project with both image folders merged (without the therm.dat file in there) and that works but the vaules I get are yet again different.

  • Momtanu (Pix4D)

    Can you try opening it with notepad++ or any other editor?

  • Isabell Eischeid

    That's what it looks like.

  • Momtanu (Pix4D)

    That means it is encoded differently. Can you reach out to Parrot? However, it is always good (increases radiometric accuracy) if you use one thermal.dat file for each project. This is because the weather conditions can change between 2 flights (though it might not be visible with human eyes). The therm.dat file should be used if you are not using targets to get absolute reflectance values. It might be that the index values/reflectance values are very different when you use two therm.dat files but the reason is that accurate radiometric correction has been done. You are also using light sensor correction, right?


    Hi there. I want to ask about the layer stack of multispectral image from micasense rededge. I have processed the multispectral images through Pix4D platform and I used the generated orthomosaic of 5 bands to do layer stacking in Envi. But why when I performed the layer stack in Envi to combine the 5 bands, the output became 2 bands?
    Please help me.

  • Momtanu (Pix4D)

    Carl, I think by stacking you mean creating a 5 band composite from the reflectance maps. Merging here means using multiple projects together to create one single project. I have replied to your question here:

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