Public Lab Research note

Packaged photo monitoring plugins available on the GitHub repositoy

by nedhorning | January 13, 2016 17:51 13 Jan 17:51 | #12582 | #12582

nedhorning was awarded the Basic Barnstar by liz for their work in this research note.

Today I added packaged Fiji/ImageJ/photo monitoring plugin software to the plugin's GitHub repository. This was done in response to a problem that prevents the photo monitoring plugin from working with the latest version of Fiji. The packaged software includes the “Fiji Life-Line version, 2014 November 25” version of Fiji (available from Fiji website:, the photo monitoring plugin and all of the required files to run it.

Installation of the software should be as simple as downloading the appropriate “.zip” file, uncompressing it then clicking on the “Fiji” icon in the newly created directory to launch Fiji. The photo monitoring plugin should be visible from the Fiji menu.

These are the bundled software packages and the platforms that are supported: Linux 32-bit: Linux 64-bit:
Windows 32-bit: Windows 64-bit: All platforms (no JRE):

NOTE: Support for OS X is coming (I don't have a Mac) but for now it is best to download the “Fiji Life-Line version, 2014 November 25” file from the website linked above and then follow the directions in the plugin installation guide. Once I am able to unpackage the OS X .dmg file I'll post that package here.

These have not been thoroughly tested so if you have problems please let me know. If you can help package the OS X files please contact me.


Thanks Ned. I haven't used the tool lately, so haven't run into the problem. Appreciate all your work on this great capability.

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I just started experimenting with my own NDVI camera rig and your posts/plugin are great. I have a question about the NDVI formula for a single camera setup. If I am using a red filter on my camera (RPI NOIR) is Near-IR light flooding the camera's blue channel? And would this IR light in the blue channel effect my NDVI reading. I am referring to an article I found online where they used the Blue channel minus the "NIR" channel as the R in NIR-R/NIR+R

Or does the IR bleed over cancel out since NDVI is a proportion.

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I couldn't follow the arguments in that paper, so I don't know whether their modified NDVI formula is valid. They know the spectral sensitivity of the camera after the IR block filter was removed and the spectral curve of the filters they added, so they should be able to come up with a correction. The focus of the paper is distinguishing vegetation from soil and their corrections are driven by that goal. If you have a similar goal and the same camera and filters, their corrections might be appropriate for you.

When you use a red filter (that blocks all blue and green light) on a full spectrum camera (e.g., RPI NoIR) the blue channel will capture mostly NIR (maybe also some UV and visible depending on the camera and filter). The blue channel is therefore highly suitable for the NIR value when calculating NDVI.

The red channel will capture lots of the incoming red and also plenty of NIR. To estimate how much of the captured light is red, you need some information about how sensitive the red channel is to red vs. NIR in the wavelength ranges you are capturing (the ranges depend on the red filter used). Without any information you can guess that maybe 30% of the red channel brightness is due to NIR and reduce the value by that much. Some other numbers might be a good guess too.

Then you would have values for how much red light was captured in the red channel and how much NIR was captured in the blue channel. But you don't know whether the sensitivity of the blue channel to NIR was the same as the sensitivity of the red channel to red. It is almost certainly not the same. Without the spectral sensitivity data for the camera, you can guess that the red channel is three times more sensitive to red as the blue channel is to NIR, and triple the value for NIR. Or use any other value you think is reasonable.

Or you can put calibration targets of known spectral reflectivity in the photos and capture camera raw images. Then adjust the pixels for the targets until the values for red and NIR match what you know they should be for the targets and then adjust all the other pixels the same way. There is more on calibration targets here.


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GIS and Icebergs - Hi Ned, I am a PhD student doing my research work on remote sensing of icebergs-- I am not sure if you will get this message but I need your advice on the best ccd camera that I can install on a Carbon Z Cub RC plane to fly over icebergs to get imagery you can reach me at it would be very nice to meet and chat with you about my project --Cheers

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Thank your for this tool Ned.

I am trying to create NDVI animations/videos using FIJI and the Photo Monitoring plug in. Here is my workflow:

  1. I record with two cameras: 1 visible, 1 in near infrared.
  2. I align and synch the two videos in Adobe Premier Pro.
  3. I export the two channels into separate directories as jpg sequences. Each directory (visible and NIR) contains a sequences of files looking something like this: name_0001; name_0002; name_0003, etc...

Here comes issue I am having: when it comes to 'creating a dual image list' using the plug-in, I get an 'exception' dialogue. I assume that this because the exported sequence now only contains the timestamp of when the file was created rather than maintaining the time stamp of when the video was shot.

I have tried to modify in bulk the timestamps of all of the images in the sequence to have the same one, however this has not worked.

My question is: Is there a way to force the plug in to create a list from the file names rather than the time stored?

This has work well with the 'single image index processing from directory' (see attached example), but I would like to make it work with my dual camera set up.

If there is any advice on how to overcome this please let me know!

Thanks! - - Stefan NDVI_color_2_1.mp4

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@liz awards a barnstar to nedhorning for their awesome contribution!

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