Photo Monitoring Plugin
photo-monitoring-plugin

![Screen_Shot_2013-06-02_at_10.38.41_AM.png](https://i.publiclab.org/system/images/photos/000/000/460/medium/Screen_Shot_2013-06-02_at_10.38.41_AM.png) [Ned Horning](http://publiclab.org/profile/nedhorning) (read [original announcement here](http://publiclab.org/notes/nedhorning/5-31-2012/registering-and-processing-photos-acquired-two-cameras)) has released an open source plugin for the cross-platform [ImageJ](http://rsb.info.nih.gov/ij/). It can produce [NDVI composites](/wiki/ndvi) from infrared and visible image pairs as well as single camera infrared filtered images. ###Features The photo monitoring plugins are written to work with Fiji image processing software (http://fiji.sc/wiki/index.php/Fiji) and they will also work with ImageJ the software on which Fiji is based. These plugins are designed to improve the efficiency and effectiveness of using infrared photos for monitoring vegetation. The plugins support dual-camera setups with one camera acquiring a "normal" visible color digital photo and the other acquiring a near-infrared digital photo and also support single camera setups such as [infrablue and super-red cameras](/wiki/infragram). The plugins provide good control of the final appearance of images via increasing the dynamic range (histogram stretching) and selecting a range of index values. ###Plugin description There are currently four plugins: **1 -** The _Create dual image list_ plugin is designed to facilitate the process of matching digital photographs that were acquired at roughly the same time. The plugin outputs a text file with the path and file names for image pairs (e.g., images acquired from two cameras) that can be input into the "Dual image NDVI processing" plugin. The image matching is done by synchronizing the times stored in image EXIF DateTimeOriginal tag from each of two cameras. If for some reason the EXIF DateTimeOriginal tag is not set then the files last modified time will be used. **2-** The _Dual image NDVI processing_ plugin is designed to co-register two images, one using a near-infrared camera and the other a “normal” visible camera. The plugin will work best if the images were acquired from two cameras mounted with their lenses close to each other, acquired at nearly the same time (so the scene hasn't changed), and it's best if the two cameras have similar characteristics such as image size and resolution. The plugin can output the following: 1. False-color infrared (CIR) image with near infrared (NIR) displayed as red, red displayed as green, and green displayed as blue 2. Normalized difference vegetation index (NDVI) image with a user-selected color table applied 3. Difference vegetation index (DVI) image with a user-selected color table applied 3. Floating point NDVI image with actual NDVI values in each pixel (data range -1 to +1) 4. A visible image clipped to the common area between the registered near-IR and visible image 5. A log file documenting the registration method used for each image pair **3-** _The Single image NDVI from directory_ plugin is designed to create color and floating point NDVI images from a directory containing images that recorded visible light in one band and near-infrared light in another. These images can be captured using the SuperBlue filter available from LifePixel (http://www.lifepixel.com/) or an [infrablue or super-red filter from Public Lab](http://publiclab.org/wiki/infragram). **4-** The _Single image NDVI from displayed image_ plugin is designed to create color and floating point NDVI images from an image displayed in ImageJ/Fiji that recorded visible light in one band and near-infrared light in another. These images can be captured using the SuperBlue filter available from LifePixel (http://www.lifepixel.com/) or an [infrablue or super-red filter from Public Lab](http://publiclab.org/wiki/infragram). ###Links * Download on GitHub: https://github.com/nedhorning/PhotoMonitoringPlugin/tree/master/downloads * View source on GitHub: https://github.com/nedhorning/PhotoMonitoringPlugin * Download ImageJ: http://rsb.info.nih.gov/ij/ * Download the friendlier Fiji version of ImageJ: http://fiji.sc/wiki/index.php/Fiji ###Color lookup tables (luts) These files assign colors to values in NDVI images created by the photo monitoring plugin. There are several luts already installed in ImageJ or Fiji, but the ones below were developed by the Public Lab community for displaying NDVI results. Copy these files into the \Fiji\Fiji.app\luts directory (in Program Files in Windows), and I guess to .../Applications/Fiji.app/luts on Mac. Then select a lut from the dropdown menu in the plugin interface. * NDVI_VGYRM.lut This lut maintains detail in the non-plant areas of a scene (NDVI = -1.0 to +0.1) which are grayscale. It colors photosynthesizing areas (NDVI = 0.1 to 0.9) with a heat map from violet to green to yellow to red. Off scale NDVI values (NDVI = 0.9 to 1.0) are colored magenta. More about this lut [here.](http://publiclab.org/notes/cfastie/08-26-2014/new-ndvi-colormap) . [![NDVI_VGYRM_lutAy.jpg](https://i.publiclab.org/system/images/photos/000/006/414/medium/NDVI_VGYRM_lutAy.jpg)](https://i.publiclab.org/system/images/photos/000/006/414/original/NDVI_VGYRM_lutAy.jpg) *Copy the image above to use as a key to your NDVI images.* . * NDVIBlu2Red.lut This lut has been used frequently for NDVI in Public Lab research notes, but the one above is probably more useful: All pixels with NDVI values below zero are colored blue. This lut will not distinguish different NDVI values between 0.1 and 0.9 as well as the one above. Below is a key to the lut above for pasting into your finished NDVI image so people have some idea what the colors mean: [![NDVIBlu2Redt.jpg](https://i.publiclab.org/system/images/photos/000/002/704/thumb/NDVIBlu2Redt.jpg)](https://i.publiclab.org/system/images/photos/000/002/704/original/NDVIBlu2Redt.jpg) . * NDVIBlu2RedWB.lut The lut below is similar to the one above, but assigns black to any pixels with the value 255 (maximum NDVI) and white to any pixels with the value 0 (minimum NDVI). It is sometimes good for troubleshooting: [![NDVIBlu2RedWBlut.JPG](https://i.publiclab.org/system/images/photos/000/002/837/thumb/NDVIBlu2RedWBlut.JPG)](https://i.publiclab.org/system/images/photos/000/002/837/original/NDVIBlu2RedWBlut.JPG) ...


Author Comment Last activity Moderation
liz "Thanks Ned! Great to hear from you :) " | Read more » almost 2 years ago
nedhorning "Hi Sam, Let me know if you are still having trouble with this. I haven't used it in years but recently got a Windows computer and can see if it's ..." | Read more » almost 2 years ago
liz "Hi there, I've shared your question with @nedhorning who created this plugin. " | Read more » almost 2 years ago
kauemv2 " Hello, I have a photo take with this kind of sensor: https://www.dropbox.com/s/7dddzda6at9d8a7/2019_0502_154807_246.JPG?dl=0 Hope that these one..." | Read more » over 3 years ago
ARMann "@warren - its probably a MAPIR Survey 3 camera: https://www.mapir.camera/collections/survey3 " | Read more » about 4 years ago
warren "Hi, can you share an image that you've taken with this camera? Where did you get the camera? Cool! " | Read more » over 4 years ago
Hala73 "Thanks for that, I'll give it a try and let you know how it worked " | Read more » over 4 years ago
Hala73 "I'll give it a try then, thanks! " | Read more » over 4 years ago
warren "We're developing a new system based on Infragram, which is more systematic, and can output things like averages, etc. We're testing this out now an..." | Read more » over 4 years ago
warren "Hi, @Hala73 - Fiji can be installed on a mac, actually -- and ImageJ (same app) on Linux. " | Read more » over 4 years ago
Hala73 "Thank you, these are plugins for PC but I'll look for something similar that works on a mac. " | Read more » over 4 years ago
cfastie "I don't think calculations at Infragram.org can be used for anything but determining the color of a new image. The Photo Monitoring plugin and Fiji..." | Read more » over 4 years ago
reversevector "I'm using an SJCam 4000, it's a cheap GoPro clone. It doesn't have custom white balance settings so I'm using incandescent with a red filter. I'm a..." | Read more » over 5 years ago
suman "I was curious to know which modified camera do you use? For my case, i am testing with Modified Mobius actioncam with wide angle A lens 87mm. If yo..." | Read more » over 5 years ago
reversevector "I'm also using VGYRM although I sometimes have to stretch the NIR value to get good results. " | Read more » over 5 years ago
suman "The macro was developed by Frank Aldiuos, a member of public labs. It basically is doing same thing as processing from the directory where all the ..." | Read more » over 5 years ago
reversevector "The Photo Monitoring plugin already has a command that generates NDVI from a folder full of images (Single image index processing from directory). ..." | Read more » over 5 years ago
nedhorning "This error will occur if you run the Create NDVI from Image plugin without having an image displayed in ImageJ. I added an error message to the nex..." | Read more » over 7 years ago
airfix4 "Thank you. " | Read more » about 8 years ago
nedhorning "At this time it is not possible to use geo-reference data. If there is sufficient interest in that functionality I could try to add it but it's not..." | Read more » about 8 years ago
airfix4 "Hello, I'm new to the organization...and NIR technology in general. I have played some with the Photo-monitoring plug in. Great too by the way! Is ..." | Read more » about 8 years ago
theowallis "Thanks for your reply Chris! " | Read more » over 8 years ago
cfastie "Theo, I have gotten that error too, even when using my own pairs of simultaneous photos (I think the cameras' clocks were way off). I forget what I..." | Read more » over 8 years ago
theowallis "Hi I am trying to process two images in Fiji, one raw infrared, one visible spectrum. When choosing the two image files from which to create a tex..." | Read more » over 8 years ago