Image Analysis Tools
Multispectral Image Calibration and Analysis Toolbox
Digital cameras can be powerful tools for measuring colours and patterns in a huge range of disciplines. However, in normal ‘uncalibrated’ digital photographs the pixel values do not scale linearly with the amount of light measured by the sensor. This means that pixel values cannot be reliably compared between different photos or even regions within the same photo unless the images are calibrated to be linear and have any lighting changes controlled for.
Some scientists are aware of these issues, but lack convenient, user-friendly software to work with calibrated images, while many others continue to measure uncalibrated images. We have developed a toolbox that can calibrate images using many common consumer digital cameras, and for some cameras the images can be converted to “animal vision”, to measure how the scene might look to non-humans. Many animals can see down into the ultraviolet (UV) spectrum, such as most insects, birds, reptiles, amphibians, some fish and some mammals, so it is important to measure UV when working with these animals. Our toolbox can combine photographs taken through multiple colour filters, for example allowing you to combine normal photographs with UV photographs and convert to animal vision across their whole range of sensitivities.
Paper: Troscianko, J. & Stevens, M. 2015. Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern. Methods in Ecology and Evolution. 6: 1320–1331.
Download & Install
This toolbox requires a working installation of ImageJ. An R installation is required if you want to generate new cone-catch mapping models. Download the version of the toolbox for your operating system, unzip the files and place them in your imagej/plugins folder. See the user guide for more specific details.
All necessary files can be downloaded from this page.
You can also watch a tutorial video on the software and photography here:
Can this software be rolled out for Android, iOS, Chromebook, or cloud processing?
This could be done, but it would mean mapping the linearisation curves and spectral sensitivities of every different mobile phone camera, so in practice wouldn’t be worth doing. Mobile phone cameras are also unable to photograph in UV, which means only a limited number of animal visual systems could be mapped to.
Can I open MSPEC images in photoshop/anything else?
No. MSPEC images are just text files that tell the toolbox how to open the RAW file(s) correctly (performing calibration and alignment). MSPEC images are opened as 32-bits per channel images, and many other software packages won’t support images with this level of detail and display them correctly if you save them in this format. Use the “Make Presentation Image” tool to produce a simple RGB colour image for saving as a standard 8-bits per channel colour image.
Why are MSPEC images shown in black & white?
Each channel of output from the camera is displayed in a separate (achromatic) slice. Scroll between the slices to see them and measure them separately. This is because the toolbox can deal with more than three channels (which would be impossible to display in colour). You can make a colour or false-colour image for presentation with the tools included (see above post).
5/9/2015 – DCRAW for Mac problem fixed (see user guide) – many thanks to Matt Henry.
7/8/2015 – Addition of photo screening tools, providing photo preview and exposure testing, and easy creation of MSPEC images. Bug fix to JND measurement tool.
29/7/15 – Bug fix – Generate Cone Catch Model wasn’t working on Windows (tested on Windows 7)