 [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) . [](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: [](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: [](https://i.publiclab.org/system/images/photos/000/002/837/original/NDVIBlu2RedWBlut.JPG) ...
| Author | Comment | Last activity | Moderation | ||
|---|---|---|---|---|---|
| suman | "Hello Ned, I tried using different exposure settings now, and its working, the pixels aren't saturated anymore. Thank you so much for your prompt ..." | Read more » | almost 7 years ago | |||
| nedhorning | "Hi Suman - Using Analyze => Measure should work. It's not uncommon to have high pixel values for bright targets. In fact if the exposure isn't s..." | Read more » | almost 7 years ago | |||
| suman | "Thank you so much for your prompt response Ned... " | Read more » | almost 7 years ago | |||
| suman | "Ohh I get it now. Actually the data has 3 calibration target, but i plan to increase it to 5 targets. I also wanted to know, how i can manually me..." | Read more » | almost 7 years ago | |||
| nedhorning | "Hi Suman - The values from 0 - 1 have been scaled from the original image. The reason I do this is that some image pixel values range from 0 - 255 ..." | Read more » | almost 7 years ago | |||
| suman | "Dear Ned Horning, I calculated image calibration coefficients, using the reflectance data from department's spectrometer and 3 calibration targets..." | Read more » | almost 7 years ago | |||
| nedhorning | "Hi - Using 440nm seem reasonable but I'd probably increase the NIR value to 760nm or beyond or something like that since the peak is probably beyon..." | Read more » | over 7 years ago | |||
| carolccarvalho | "Hello, @nedhorning, for the Rosco Roscolux #2007 Storaro Blue Gel Filter, with the following datasheet Could I just use the visible reflectance ..." | Read more » | over 7 years ago | |||
| Davidkao | "Thank you very much for the advice Chris and Ned, I have learned a lot. I will continue to this research, so if possible if I encounter any problem..." | Read more » | almost 8 years ago | |||
| cfastie | "David, When using a blue (#2007) filter, the red channel records NIR and the blue channel records visible blue light which is used to compute NDVI...." | Read more » | almost 8 years ago | |||
| nedhorning | "Hi David - This is an interesting project. The reflection of the glass should affect the results as long as the reflection is not in the area of yo..." | Read more » | almost 8 years ago | |||
| Davidkao | "Hello, @nedhorning, I had recently been researching about NDVI and came across your amazing calibration plugin. It works great; however I have a fe..." | Read more » | almost 8 years ago | |||
| nedhorning | "The current version of the plugin only outputs index (NDVI and DVI) images. The plugin only calibrates two bands, a visible and a NIR band and two ..." | Read more » | over 8 years ago | |||
| JacobNederend | "Thanks for the feedback. I think I misunderstood the function of this plugin. I thought I could calibrate my jpeg R/G/NIR images to a black, a gre..." | Read more » | over 8 years ago | |||
| nedhorning | "Hi Jacob, To check for aperture you could try another EXIF reader. Maybe "max aperture" is the same as "aperture" but I have no idea. When working ..." | Read more » | over 8 years ago | |||
| JacobNederend | "Hi Ned, I am really excited about the work you are doing here as it helps resolve some major issues with my grad studies. I have a few questions: ..." | Read more » | over 8 years ago | |||
| nedhorning | "Unfortunately those values would only work if you had the same materials that I used. To get the reflectance values you would either need to fine s..." | Read more » | over 8 years ago | |||
| aldehyde | "How to get target reflectance values for the visible and near-infrared wavelengths that correspond with the camera filter? Can I use?. 0.7529225,0..." | Read more » | over 8 years ago | |||
| nedhorning | "Hi aldehyde - Did you look at the user guide on Github: https://github.com/nedhorning/PhotoMonitoringPlugin that should have information about crea..." | Read more » | over 8 years ago | |||
| aldehyde | "Please help. If it is possible to describe all the work with the plugin. How to create "сomma-separated variable (CSV) file with the reflectance v..." | Read more » | over 8 years ago | |||
| nedhorning | "Mathew - Have you been able to find a reflectance plot for those paints? I looked but didn't see it. Other paints I was looking at a couple years a..." | Read more » | over 8 years ago | |||
| mathew | "Rosco manufactures outdoor-grade TV paints including 60% grey (TV white) and black (3%) and chroma colors (blue, green). They would be good choices..." | Read more » | over 8 years ago | |||
| admaltais | "Have you considered using reference charts used to calibrate green rooms in cinema? Some thing like this: labsphere - Reflectance Reference Targets..." | Read more » | over 8 years ago | |||
| warren | "This is something that'd also benefit the general white balance process of Infragram cameras. I wonder, are there any paint sample strips that are ..." | Read more » | over 8 years ago |