{"id":2402,"date":"2015-07-21T18:56:05","date_gmt":"2015-07-21T18:56:05","guid":{"rendered":"http:\/\/www.richardmudhar.com\/?p=2402"},"modified":"2016-08-18T12:51:25","modified_gmt":"2016-08-18T12:51:25","slug":"using-near-ir-to-look-for-photosynthesis-and-plant-health-with-ndvi","status":"publish","type":"post","link":"https:\/\/www.richardmudhar.com\/blog\/2015\/07\/using-near-ir-to-look-for-photosynthesis-and-plant-health-with-ndvi\/","title":{"rendered":"Using near IR to look for photosynthesis and plant health with NDVI"},"content":{"rendered":"

The NoIR Raspberry Pi camera<\/a> comes with a blue filter to do near infrared photography – the blue filter ices the visible red but passes near IR which records as red, apparently.<\/p>\n

\"NDVI<\/a>
NDVI image of something in the polytunnels. Should have made a not of what this plant is \ud83d\ude09 Anyway, more red and going to magenta white overload=more photosynthesis<\/figcaption><\/figure>\n

NDVI (Normalized Difference Vegetation Index<\/a><\/em>) is the near IR plus red divided by near IR minus red. Take a look at this image<\/a> for the meaning of the colours – red, magenta and white is more photosynthesis, cool colours and black are less. Chlorophyll uses red but doesn’t use near IR which it reflects, hence the difference carries useful information.Lots more<\/a> at Public Lab<\/a>. <\/p>\n

So I thought I might use this to look for plant health at The Oak Tree. My NoIR Rpi camera was out in the field so I was looking for a different way to do this using a regular camera to take two images. The blue filter starts off bad by throwing out the red channel, but in some of the older Public Lab stuff there is a way of integrating two photos-\u00a0 one a bog-standard RGB pic and the other a picture taken through an IR filter. I have a B&W IR filter<\/a> that looks almost black so I shot pictures with the filter and without filter, both using a tripod, then used Ned Horning’s photo monitoring plugin<\/a> for Fiji image processing to do the grunt work of matching the two images up.<\/p>\n

The NRG image has its own charm and is reminiscent of IR film days – I think the IR is added to the red but I am not sure<\/p>\n

\"The<\/a>
The NRG image has its own aesthetic.<\/figcaption><\/figure>\n

The normal colour image is this<\/p>\n

\"The<\/a>
The real colour image.<\/figcaption><\/figure>\n

Exposure times through the IR filter are shockingly long, presumably because the camera IR stop filter is fighting what residual gets through. There is a case to be made for using a raspberry Pi or perhaps two to take simultaneous pictures, one with the NoIR and the IR filter and the other with the regular Pi camera.<\/p>\n

\"from<\/a>
from a different angle, NDVI<\/figcaption><\/figure>\n
\"The<\/a>
The flowers are doing quite well<\/figcaption><\/figure>\n
\"Flowers\"<\/a>
Flowers, NDVU (red is more photosynthesis)<\/figcaption><\/figure>\n","protected":false},"excerpt":{"rendered":"

The NoIR Raspberry Pi camera comes with a blue filter to do near infrared photography – the blue filter ices the visible red but passes near IR which records as red, apparently. NDVI (Normalized Difference Vegetation Index) is the near IR plus red divided by near IR minus red. Take a look at this image … Continue reading “Using near IR to look for photosynthesis and plant health with NDVI”<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[275,300,10,14],"tags":[311,310],"class_list":["post-2402","post","type-post","status-publish","format-standard","hentry","category-greenmantle","category-photography","category-raspberry-pi","category-smallholding","tag-infrared","tag-ndvi"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p5aOO7-CK","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/posts\/2402","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/comments?post=2402"}],"version-history":[{"count":3,"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/posts\/2402\/revisions"}],"predecessor-version":[{"id":2725,"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/posts\/2402\/revisions\/2725"}],"wp:attachment":[{"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/media?parent=2402"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/categories?post=2402"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.richardmudhar.com\/blog\/wp-json\/wp\/v2\/tags?post=2402"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}