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Detection of grapevine trunk disease Esca by hyperspectral imaging
Leaves of grapevine diseased with Esca (courtesy Wikipedia)

Global viticulture loses more than £1 billion every year due to so-called grapevine trunk diseases (GTD). Some vineyards just suffer a lower yield whereas others can lose the whole vineyard. Esca is one of three main GTD diseases. Unlike the usual seasonal problems such as downy or powdery mildew, GTD have no known treatment or cure. Sodium arsenite (NaAsO2) was used in the past to control GTD but due to its wide toxicity and accumulation in the environment, its agricultural use has been banned.

One of the perplexing features of Esca is that some leaves on a vine may be affected while others appear healthy; one year a vine may look very sick with highly discoloured leaves but the next year appear healthy. Usually it is a chronic disease but can cause sudden death in just a few days with little advanced warning.

Anna Kicherer and colleagues at the Institute for Grapevine Breeding in Siebeldingen, Germany have recently reported the use of hyperspectral leaf imaging to monitor Esca in a vineyard in Germany. Writing in the journal Plant Methods they compared aerial and land-based methods of recording the reflectivity of grapevine leaves. Spectral imaging techniques have the advantage that they are non-invasive, non-destructive and can characterise crops quickly. They give what medics call a presumptive diagnosis based on the appearance of disease rather than identifying a specific pathogen with a genetic test. Nonetheless this can be very valuable as spectral imaging is quantitative, objective and contains more information than visual inspection.

As Sir Isaac Newton said, the human eye is a wonderful invention but it sees only three colours: red, green and blue. Multispectral imaging has the advantage that it sees 5-7 different colour bands from the near ultraviolet (UV) to the near infrared (NIR). Hyperspectral imaging goes further and can comprise hundreds of different colour bands from the UV (400 nm wavelength light) to NIR (1000 nm wavelength light) and infrared (IR). The Siebeldingen group therefore made a comparison of visible-NIR and IR hyperspectral imaging in the vineyard and multispectral imaging from an Unmanned Aerial Vehicle (UAV) flown over the vineyard. Small, light weight multispectral cameras can be carried by drones but heavier hyperspectral cameras need to be used on the ground. They also modelled the potential optimisation of carefully chosen hyperspectral bands to measure Esca disease in vines.

To gather the hyperspectral images of vines in a local vineyard, Kicherer and team used a modified tractor equipped with imaging cameras and GPS. The figure below shows how it was deployed in the vineyard. The tractor was equipped with additional bright light sources and spectral cameras.

The vine tractor straddling a row of vines (a) and imaging as it moves (b) (courtesy Julius Kühn-Institut and BMC Springer Nature)

It was known at the outset that the vineyard had an incidence of around 11% Esca in the vines. Vines were imaged biweekly during the growing seasons over a three year period. Spectral imaging immediately revealed differences between healthy leaves and those affected by Esca as shown below.

Spectral reflectance of vine leaves affected by Esca and healthy controls (courtesy Julius Kühn-Institut and BMC Springer Nature)

Infected leaves clearly reflect more NIR light (700-1000 nm) and yellow to red light (550-650 nm). Much smaller changes were seen in the IR wavelength range measurements. Taking measurements from two of the three years of study, it was possible to create a machine learning model to identify vine leaves showing Esca. By adding information about which leaves came from infected vines it was possible to improve the classification of the infected and healthy vines. In the best case, using visible-NIR hyperspectral data from two years and applying the model to the third year: classification was 82% accurate, the true positive rate was 85% and the false positive rate was 14%.

Encouraged by these results, Kicherer and team tested the classification model on pre-symptomatic Esca infected vines. They reported 73-81% classification accuracy, 69-100% true positive rate and 20-26% false positive rate. Finally they beat the human eye!

Perhaps in the future vineyards will be able to use spectral imaging to eradicate Esca infected vines before infection spreads to the rest of the plants.

The Plant Methods paper also contains further information on UAV measurements and ideas for future multispectral imaging approaches. To find out more, read the Open Access document here. Further information on Esca and other GTD is available in EU sponsored YouTube videos.

Figures are reproduced courtesy of a Collective Commons licence from Julius Kühn-Institut and BMC Springer Nature.


Italian vineyards investigated with Google Earth
italian vineyards map
Locations of vineyards in Italy (courtesy Elsevier and University of Padova)

At the end of the old year journalists like to write articles summarising events, listing items, totalling numbers. At the beginning of the New Year writers and readers alike become more philosophical, resolving to extract information from mere data and wisdom from observations. Google Earth has been a phenomenal source of data for many years but now a group from the University of Padova have just reported how to use Google map data to quantify how and where Italian farmers are tending their vineyards.

With a few Open Source software tools, Alessia Cogato and her colleagues gained real insight into viticulture throughout Italy from satellite image data from Google Earth. The potential wisdom from the study is to establish: how many Italian vineyards could be mechanised to improve efficiency; where they are located; and what type of mechanisation should be employed.

According to an old English book on horticulture, pruning vines is rated difficult compared to other crops. There are various methods of cultivation, training vines either vertically (Free-cordon and Geneva Double Curtain) or horizontally (Pergola and Tendone). Vertical cultivations are typically much easier to mechanise therefore local viticulture tradition is an important parameter in improving efficiency.

Other effective parameters (which can be different from one vineyard and region to another) are: the spacings between rows; the amount of spare land at the end of a row to turn a tractor; and the slope of the vineyard. The Padova group devised a Level of Mechanisability index which takes account of all the parameters to assess the viability of improving the efficiency of vineyards by mechanisation.

So how did they glean the required information from Google Earth data?

QGIS Open Source software screenshot

Geography today is a sophisticated science, far from ‘advanced colouring in’ as some snooty physical science students used to refer to it. Displaying geographical data, mining the data and analysing the data is the work of a Geographic Information System (GIS). The team used QGIS to analyse image data from Google Earth. QGIS is an Open Source project available for Windows, Linux and Mac OS platforms. QGIS allows multiple layers of earth data from different sources to be displayed, correlated and analysed.

Italian vineyard parameterisation (shape headspace LxW ratio row spacing) and cultivation (inset) (courtesy Elsevier and University of Padova)

QGIS was also used to import and analyse terrain slope data from the Institute for Environmental Protection and Research of Italy (ISPRA).

Slope data for terrain in Italy derived from satellite images (courtesy Elsevier and University of Padova)

Combining all of the key parameters from the raw image data, Levels of Mechanisability were calculated for each of the 3686 vineyards in the Padova study.

With vineyards in southern Europe under pressure from climate change and a global pandemic, sustainable cultivation methods are more important than ever. Looking forward into the New Year, the Padova team will hope government agencies apply some wisdom derived from their information based on Google satellite data.

The data report published by Elsevier can be found here. A full report of the study can be found in the Journal Land.

Images from Elsevier and University of Padova used courtesy of the Creative Commons licence.


Climate change: a challenge or an opportunity for viticulture?
Vineyards in Adelaide, Australia

October is the time most vineyards have completed the harvest and wineries start the winemaking process. Some wineries are counting a better than ever harvest but others are just counting the cost. This summer the fields of Australia, California, South Africa, Portugal and even Oregon have been ravaged by fire and drought. This year the fields of the United Kingdom and even southern Sweden have been blessed by a long hot summer and exciting prospects for this year’s vintage.

Can innovation offer viticulture a solution to the challenges of climate change? Can innovation realise the opportunities created by climate change?

Three years ago the European Union commissioned the Clim4Vitis project, aiming to mitigate the effects of climate change on European Viticulture. Since its inception the original five member consortium has grown to 200 worldwide members and resulted in the Porto Protocol: Climate Talks.

European Union project 810176 Clim4Vitis

Despite COVID-19, the innovation phenomenon that is Zoom permitted open international discussion of water shortage, pests and diseases, and increased weather variability. During one recent virtual workshop we discovered climate change in Argentina is being mitigated by moving cultivation to higher elevations. Problems and solutions are being shared through on-line networking. Collaborations have been established between local vineyards in Argentina and viticulturalists from Chateau Lafite estates in France. Nobody has all the answers but it seems it’s good to talk!

In Portugal, the FREND project has developed an innovative technology platform for precision viticulture. Precision Agriculture (PA) has been growing in importance for the cultivation of many crops. Through the use of plant characterisation and artificial intelligence, PA offers accurate and timely delivery of water, nutrients and chemical interventions when needed.

According to Antonio Cardoso, CEO of XpectralTEK (FREND project coordinator), their precision viticulture platform has measurable benefits.

In vineyards around Braga we have seen a 20% reduction in the use of water, a 60% reduction in the incidence of disease and a 2% increase in potential grape alcohol as a result of using the FREND viticulture platform.

Antonio Cardoso CEO XpectralTEK

Climate change is posing problems but agricultural innovation is providing solutions. For many climate challenges there are innovative opportunities.

In the UK, vineyard managers have seen many positive opportunities due to climate change. Historically, England was not viewed as a place to produce quality wine. In part this was due to cultivation of grape varieties that would withstand the vagaries of the UK weather. Nobody in southern Europe would choose to grow grape varieties like Bacchus or Reichensteiner. Today however English and Welsh vineyards are growing champagne grapes pinot noir, chardonnay and meunier.

Still and sparkling white wines of outstanding quality are now produced in England. Two Best in Show Decanter World Wine Awards were given to Roebuck Estates and Simpsons Wine Estate this year (2020).

Thanks to expert viticulture and a warming climate, even red wine can be successfully made in England. Lyme Bay Winery in Devon reported a record 14.7% potential alcohol in pinot noir grapes from the 2020 harvest. Greater day length in the North combined with hotter, extended growing seasons now offer a real opportunity for expert wine producers in the South to expand north.

Global climate change will continue to cause chaos and bring challenges to the world of wine. It also brings powerful global reasons to exchange experience and opportunities to innovate solutions. And continue to make excellent wine.