Posted by
TimFeinstein on
Jul 22, 2016; 12:53pm
URL: http://imagej.273.s1.nabble.com/Help-for-a-new-user-to-analyze-percentage-of-certain-colored-pixels-in-digital-image-tp5016922p5016925.html
Professional color analysis can get very sophisticated, so it is a
question of how much precision you need (and can afford). In my view much
of your effort should focus on standardizing the acquisitions. Acquiring
your images in RAW mode with standard settings will help, but that still
leaves a lot of variables, especially if your plants are in a greenhouse
rather than a fully light controlled grow space. Your workflow should
include a standardized color correction process, meaning a color card that
you include in each photo with a software that detects the card and
automatically corrects it. For example here is a workflow that uses the
widely used X-Rite color checker and Rawtherapee, a free and open-source
alternative to Adobe Lightroom.
https://stephenstuff.wordpress.com/2012/07/06/digital-camera-profiling-with-raw-therapee-and-argyll-cms/
I suggest you color correct the RAW files in Rawtherapee, then export as
TIFFs to analyze in ImageJ/Fiji. This can almost certainly be automated
to let you process large batches of data at once.
If you are working in a greenhouse, weather conditions will dramatically
change your results. In that case think about using flash lighting rather
than ambient. Naked camera flashes cause bright spots that would ruin
your data; for your purposes I'd recommend a diffused ring light (see
example below) at a set distance from the plant.
http://www.bhphotovideo.com/c/product/996516-REG/roundflash_roundflashmb_magnetic_black_rigflash_adapter.html
Best,
Tim
Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology
On 7/21/16, 10:51 PM, "ImageJ Interest Group on behalf of Emily Teng"
<
[hidden email] on behalf of
[hidden email]> wrote:
>Hi everyone,
>I am completely new to ImageJ. Just found out about it today and hoping
>it
>is exactly what I need for my research purposes. I am a PhD student.
>
>I need a method to analyze the percent of coloration of poinsettia plants
>over time. I plan to take digital photos of the top of the canopy over
>time and analyze those images. As I understand it, I could use ImageJ for
>this purpose correct?
>
>Taking for example, a red poinsettia - I would need the program to count
>all the pixels that are any shade of red (vs green) in the plant.
>
>
https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.ecke.c>om%2fpoinsettias%2fbractmeter%2f&data=01%7c01%7ctnf8%40pitt.edu%7cfa4db3a9
>12dd46e5129c08d3b1dcaa28%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=69bn
>gVNCr%2bGvhlbT3U7xLAmQ2ASxHI9LPYWP0EYVtxw%3d
>
>That is what I'm trying to do. The professor who created that told me he
>had someone do programming to count the pixels. But I'm thinking ImageJ
>will be able to do this if I know how to use it?
>
>Can someone tell me
>1. Can ImageJ do this?
>2. If yes - Point me in the direction of how I should go about learning
>how to do this?
>
>Thank you in advance for any help and guidance.
>
>Emily
>
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