Publications & processing help

The Global LAI project is still in its start-up phase. We presented first results from the project at the ATBC in Cairns, 2014. The presentation can be downloaded here: Pfeifer et al. 2014. We presented on mapping ecosystem functions in tropical landscapes at the Tropical Ecology Meeting in Goettingen, 2016. We also presented at the GFBI conference in Beijing, September 2017. The presentation can be found here: 2017_Beijing_GFBI

Protocols and templates for use in the field:

Protocol for sampling including setting the context. Pfeifer_2015_Protocol_LAI_Measurements_V3.0

Field recording sheet: here it is

Protocols and templates for adding data to global database

We have developed a template that makes the transfer of your data into the Global LAI Database as easy as feasibly possible. You just need to download the highlighted excel template file below to see all sheets. There are two options available to you:

(Option A) You simply sort your plot images into plot folders and send them to us for processing using the Caneye software. Please enter metadata (yellow fields) into the templates in this excel file and save the DataFieldSheet as *csv and the TripIDSheet as *csv. Send both together with the image data sorted into folder to us (marion.pfeifer@ncl.ac.uk) make the analyses possible without us asking too many questions: LAI_Template_Infos

(Option B) You do the sorting and then also the analyses on the images yourself using below processing codes. You extract the data (Note: we will upload an R code allowing you to extract the Caneye output files including html and excel files quick and easy) and add them to the templates (green fields in above two template sheets See Option A for access to the templates). Then you send the final datasheets to us for checking and adding to the database.

We will send all final datasheets to you, whichever option you choose. You will have access to all other data in the database after sending a project description to us first stating title and objectives and very brief summary of project . We will send that description out to everyone and if we don’t hear otherwise will assume everyone is happy to share their data.

Code (Matlab) & helpfile explaining code and more for processing images in the lab to derive canopy structure estimates: Code 1 (one exposure per sample point), Code 2 (three exposures per sample point). Both need this isodata file if you are using the Ridler and Calvard Thresholding as specified in the code. You can modify the code to add another thresholding algorithm. Here is the helpfile that shows the code, information on how to edit code and details the main CanEye steps as used in the Global LAI project. If you don’t have Matlab and know your way around Python: try this file produced by PhD student Daniel A. da Silva. Download the latest version (updated 13/12/2018) from the google drive here: https://drive.google.com/open?id=1C2AXq_5bAwfxX8F6PyncAM0RPVIxF6J1.

Important: If you struggle to get the download to work from the CanEye project webpages (https://www6.paca.inra.fr/can-eye/): (1) Go to Download tab, (2) Scroll down to Licence Agreement, agree and continue, (3) If you fail to read something in that licence agreement window: copy the agreement php listed there (http://w3.avignon.inra.fr/can-eye-inscription/licence.php) and paste into a new window of your internet search engine. That did the trick for us.

Publications:

  1. Pfeifer M, Gonsamo A, Disney M, Pellikka P & Marchant R. 2012. Leaf area index for biomes of the Eastern Arc Mountains: Landsat and SPOT observations along precipitation and altitude gradients. Remote Sens Environ 118: 103 – 115. Contact us if you want a copy. Link
  2. Pfeifer M, Disney M, Quaife T & Marchant R. 2011. Terrestrial Ecosystems from space: a review of earth observation products for macroecology applications. Global Ecol Biogeogr 21: 603 – 624. Contact us if you want a copy. Link
  3. Pfeifer M, Lefebvre V, Gonsamo A, Pellikka P, Marchant R, Denu D & Platts PJ. 2014. Validating and linking the GIMMS leaf area index (LAI3g) with environmental controls in East Africa. Remote Sens. 6: 173 – 1990. Open Access. Download
  4. Hardwick S, Toumi R, Pfeifer M, et al. 2015. The relationship between leaf area index and forest microclimate. Agr For Meteor 201: 187 – 195. Contact us if you want a copy. Link
  5. Pfeifer M, Kor L, Nilus R, Turner E, Cusack J, Lysenko I, Khoo M, Chey VK, Chung AC, Ewers RM. 2016. Mapping the structure of Borneo’s tropical forests across a degradation gradient. Remote Sens Environ 176: 84-97. Contact us if you want a copy. Link
  6. Shirima D, Pfeifer M, Platts PJ, Totland O & Moe Stein R (2015) Interactions between Canopy Structure and Herbaceous Biomass along Environmental Gradients in Moist Forest and Dry Miombo Woodland of Tanzania. PLOS One 10. Open Access. Link
  7. Pfeifer et al. 2018. Tropical forest canopies and their relationships with climate and disturbance: results from a global dataset of consistent field-based measurements. Forest Ecosystems 5:7. Open Access. Link.

 

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