PhytoSim used to analyse the effect of mistletoe on Scots pine

on January 20th 2012 a paper was published that used a model, implemented in PhytoSim, to analyse the effect of mistletoe on Scots pine.

Reference:

Zweifel R., Bangerter S., Rigling A. and Sterck F.J. (2012). Pine and mistletoes: how to live with a leak in the water flow and storage system? Journal of Experimental Botany, 63(7), 2565-2578.
http://jxb.oxfordjournals.org/content/63/7/2565.abstract

Abstract:

The mistletoe, Viscum album, living on Scots pine (Pinus sylvestris) has been reported barely to regulate its transpiration and thus heavily to affect the gas exchange of its host. The extent of this mistletoe effect and its underlying mechanism has, so far, only been partially analysed. In this study, pine branches with different mistletoe infestation levels were investigated by sap flow gauges and analysed with a modelling approach to identify the mistletoe-induced stomatal regulation of pine and its consequences for the water and carbon balances of the tree. It was found that Viscum album barely regulates its stomata and that pines consequently compensate for the additional water loss of mistletoes by closing their own stomata. Despite the reduced stomatal aperture of the needles, the total water loss of branches with mistletoes increased. Furthermore, the increasingly closed stomata reduced carbon assimilation for the pine. Such a negative effect of the mistletoes on pine’s stomatal conductance and carbon gain was particularly strong during dry periods. Our study therefore suggests that mistletoe-induced stomatal closure is a successful mechanism against dying from hydraulic failure in the short term but increases the risk of carbon starvation in the long term. With the current conditions in Valais, Switzerland, a tree with more than about 10–20% of its total leaf area attributable to mistletoes is at the threshold of keeping a positive carbon balance. The currently increasing mistletoe abundance, due to increasing mean annual temperatures, is therefore accelerating the ongoing pine decline in many dry inner-Alpine valleys.

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PhytoSim 2.0 Released

Version 2.0 of PhytoSim has been released. Download it here.

These are the new features/changes and fixes:

General:

  • CHANGED: Simplified Module Manager, all modules are now built-in (faster startup, no additional downloads required).
  • CHANGED: New PhytoSim software update mechanism.
  • CHANGED: The Help > Support dialog has been removed. Contact support@phyto-it.com for support related questions.
  • CHANGED: Support for multiple simultaneously running PhytoSim instances per account (default is still 1 instance).
  • FIXED: Mac OS X Snow Leopard is supported again.
  • FIXED: Bug for workspaces within a folder structure with folder names containing special characters.

 Data I/O Module:

  • NEW: Embedded data input type. Embed data directly in the workspace: enter manually, copy-and-past or drag-and-drop selected data from text files or Excel).

 Modelling Module:

  • NEW: Fractional units, e.g. cm^3/2.
  • NEW: New unit ‘#’, representing a count or a number of items. E.g. 20 #[plants].m^-2[ground].
  • NEW: New crop model: SUCROS1 (Simple and Universal CROp growth Simulator).
  • CHANGED: The valueat( x, at ) function for data variables now uses the data variable independent variable for the ‘at’ argument instead of the model independent variable.
  • FIXED: Sort order violation for algebraicVariable = previous( algebraicVariable ) or valueat( algebraicVariable, t ).

 Simulation Module:

  • NEW: Graph curves can be put on the second Y-axis.
  • NEW: Logarithmic scales on the Y-axes.
  • NEW: SUCROS1 crop model example showing embedded data inputs and advanced use of the valueat() function.
  • FIXED: Scroll wheel zooming no longer zooms out beyond the graph data.
  • FIXED: Potential crash when zooming in on graphs.

 Calibration Module:

  • CHANGED: Faster calibration when the simulation period is only a small part of the available data period.
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Phyto-IT @ the 9th International Workshop on Sap Flow

Phyto-IT demonstrated its products (Sap Flow Tool, PhytoSim, …) at the 9th International Workshop on Sap Flow (June 4-7 2013, Ghent, Belgium).

The main topic at the conference were:

  • Measurement methodologies
  • New insights in hydraulic plant functioning
    (drought stress, water (uptake) pathways, climate change)
  • Limitations in the hydraulic pathway (cavitation)
  • Modelling water transport (xylem, phloem)
  • Irrigation and other practical applications

Phyto-IT @ the 9th International Workshop on Sap Flow

The Phyto-IT booth.

Phyto-IT @ the 9th International Workshop on Sap Flow

Talking about our technology.

Thanks to all the participants who came by our booth!

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Sap Flow Tool 1.4 Released

Sap Flow Tool 1.4 has been released. The new version can be downloaded here (free 30-day trial available).

New features:

  • Online authentication system, no need for USB dongles as long as you are online.
  • Free 30-day trial of the full version.
  • New ‘Check for updates’ system with built-in download and install.
  • Windows 8 compatibility.

Note: Existing customers should also create an account which will then be switched to the full version of Sap Flow Tool.

Overview video:
http://www.youtube.com/watch?v=16WYkV4UDqk

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Phyto-IT sponsors the 9th International Workshop on Sap Flow

Phyto-IT will be sponsoring the 9th International Workshop on Sap Flow. It will be held in Ghent, Belgium from June 4-7 2013.

More information can be found here:

http://www.sapflowworkshop.info

and the conference flyer can be downloaded here:

http://www.sapflowworkshop.info/documents/flyer_9thsapflowworkshop.pdf

 

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PhytoSim @ HortiModel 2012

Phyto-IT demonstrated its PhytoSim modelling and simulation software at the HortiModel 2012 conference (Nanjing, China, November 4-8, 2012).

The HortiModel 2012 conference was the Fourth International Symposium on Models for Plant Growth, Environmental Control and Management in Protected Cultivation. It covered a wide range of topics related to horticulture:

  • Crop and Climate Management
  • Water, Nutrient and Energy Management
  • Decision Support and Farm Management
  • Product Quality
  • Systems Biology, Gene-plant-crop Modelling
  • 3D-models, Architectural Models
  • Methodological Issues, Aggregation and Scale
  • Combination of Models and Sensors

HortiModel 2012

HortiModel 2012 booth

Thanks to all the participants who came by our booth!

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Sap Flow Tool 1.3 Released

Sap Flow Tool 1.3 has been released. It is a major release which includes some of the most requested features to date: importing and visualising non-sap flow data (even non-ICT International data) and custom graphs for combining data from multiple sensors and/or files.

The new version can be downloaded here (including a demo version).

New features:

General

  • NEW “visualise module”: custom graphs, display data from multiple sensors and files (even non-ICT International data).
  • Value inspector slider on all graphs: shows numerical value of all curves at the slider position.
  • Option to show DOY on graph x-axis.
  • Ability to search in the user manual.

Files window

  • Import any data file (sap flow calculations still limited to ICT International .csv and .bin files).
  • Quick view graph: plot the currently selected item in the Files window.
  • Batch import of multiple data files + drag & drop in the Files window.
  • Batch export of multiple sensors.
  • Auto-reimport exported data.
  • Merge data from the same sensor in different files.
  • Files window filter: show only items that match certain criteria.
  • Move files up and down in the Files window.

Visualise module

  • Custom graphs, display data from multiple sensors and files.
  • Apply data filters to any curve on the graph.
  • Export all data from the custom graphs.
  • New example: sample 6, shows the use of custom graphs and non-sap flow data.

Overview video:

http://www.youtube.com/watch?v=Rvw2Bc5uMkc

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PhytoSim used in sap flow research

In a recently published paper about a new sap flow measurement technique (Sapflow+) PhytoSim was used to develop, simulate and calibrate the Sapflow+ model. Besides that, the PhytoSim sensitivity and identifiability analysis was also used to determine if the heat velocity, volumetric heat capacity and thermal conductivities could be estimated from the measured data.

Reference:

Vandegehuchte M.W. and Steppe K. (2012). Sapflow+: a four-needle heat-pulse sap flow sensor enabling nonempirical sap flux density and water content measurements. New Phytologist, 196(1), 306-317. http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04237.x/abstract

Abstract:

  • To our knowledge, to date, no nonempirical method exists to measure reverse, low or high sap flux density. Moreover, existing sap flow methods require destructive wood core measurements to determine sapwood water content, necessary to convert heat velocity to sap flux density, not only damaging the tree, but also neglecting seasonal variability in sapwood water content.
  • Here, we present a nonempirical heat-pulse-based method and coupled sensor which measure temperature changes around a linear heater in both axial and tangential directions after application of a heat pulse. By fitting the correct heat conduction–convection equation to the measured temperature profiles, the heat velocity and water content of the sapwood can be determined.
  • An identifiability analysis and validation tests on artificial and real stem segments of European beech (Fagus sylvatica L.) confirm the applicability of the method, leading to accurate determinations of heat velocity, water content and hence sap flux density.
  • The proposed method enables sap flux density measurements to be made across the entire natural occurring sap flux density range of woody plants. Moreover, the water content during low flows can be determined accurately, enabling a correct conversion from heat velocity to sap flux density without destructive core measurements.
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PhytoSim used in wood thermal diffusivity research

A recently published paper on wood thermal diffusivity used PhytoSim to calibrate a theoretical model in order to determine both axial and tangential diffusivity in sapwood. The PhytoSim sensitivity and identifiability analysis was also used to better understand the model and learn which parameters most influenced the end-results.

Reference:

Vandegehuchte M.W. and Steppe K. (2012). A triple-probe heat-pulse method for measurement of thermal diffusivity in trees. Agricultural and Forest Meteorology, 160, 90–99.
http://www.sciencedirect.com/science/article/pii/S0168192312000998

Abstract:

Although thermal diffusivity is a crucial parameter for sap flow calculations in both the heat field deformation and the heat ratio method, it is seldom measured on a routine basis. This paper presents a theory based on thermodynamic principles to determine both axial and tangential diffusivity in sapwood. By measuring the temperature response after application of a heat pulse at a short axial and tangential distance from a line heater, axial and tangential thermal conductivity as well as volumetric heat capacity of the sapwood can be derived from a theoretical model. From these parameters, axial and tangential diffusivity can easily be determined. Sensitivity analysis and results of an experiment on European beech (Fagus sylvatica L.) confirm the applicability of the method. The obtained thermal diffusivities ranged from 2.7 × 10−7 m2 s−1 to 2.2 × 10−7 m2 s−1 for a relative water content (moisture per dry weight) ranging from 0.47 to 0.90, respectively. This was on average 22% lower than when applying the common methodology based on wood core sampling.

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PhytoSim used in leaf temperature modelling research

A recently published paper on leaf temperature monitoring and modelling used PhytoSim as the main modelling and simulation software. The PhytoSim built-in sensitivity, identifiability and uncertainty analysis was used to help construct a model for online plant stress detection at the leaf level.

Reference:

Vermeulen K, Aerts J-M, Dekock J, Bleyaert P, Berckmans D, Steppe K. (2012). Automated leaf temperature monitoring of glasshouse tomato plants by using a leaf energy balance model. Computers and Electronics in Agriculture 87: 19–31. http://www.sciencedirect.com/science/article/pii/S0168169912001172

Abstract:

In order to detect biotic and abiotic stress at leaf level thermal indices based on leaf temperature measurements have been commonly used. The application of these indices within glasshouse crops is, however, restricted due to the specific humid conditions and the large spatial variability of irradiance and air temperature inside a glasshouse. In this study, a novel diagnostic algorithm is proposed as an alternative method to automatically monitor the leaf temperature of a glasshouse tomato crop based on the ecophysiological interactions between a leaf and its surrounding microclimate. Given that this algorithm is intended to be implemented as a software tool in glasshouse climate control systems, a critical overview of all relevant equations found in literature was first given. Next, the most appropriate equations were selected by using two objective criteria, i.e. the commonly used R2 and the less conventional Young Information Criterion, which also takes into account the complexity of an algorithm, so that the most feasible algorithm for automated monitoring purposes was built. Our results also showed that an in situ calibration of the selected algorithm was needed, for which a novel procedure was proposed. Once calibrated, this algorithm successfully simulated the leaf temperature of a well-watered tomato plant during several days given that the environmental conditions in its microclimate were accurately measured. Finally, the 95% confidence limits on the leaf temperature simulations provided the requested dynamic thresholds necessary for an effective automated monitoring tool. It was demonstrated that by using this novel diagnostic algorithm unexpected and likely harmful stomatal closure can be detected before visual signs of turgidity loss are observed.

 

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