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Table 1 State-of-the-art high throughput shoot phenotyping software tools

From: Holistic and component plant phenotyping using temporal image sequence

Software name

Plant part

Language

Target plant

Phenotype

Image type

Analysis technique

Comment

HTPheno [21]

Shoot

Java, ImageJ

Maize

x-extent, y-extent, diameter, width, height, projected shoot area

RGB

Open source, automated

Fails to handle changing light conditions and multiple zoom levels

Canopy reconstruction [22]

Shoot

C# using .NET

Rice, wheat

Shape and surface area of the leaf, shoot architecture (3D modeling)

RGB

Open source, automated

Multiple images captured using single camera from different angles. VisualSFM used to generate camera calibration and PMVS for point cloud generation in 3D reconstruction. Effected by occluded leaves or overlapping surfaces

Integrated analysis platform (IAP) [23]

Shoot

Java, ImageJ

Barley, maize, Sorghum

Morphological parameters, and watering status

RGB,F,NIR

Open source, semi automated

Supports cluster computing and can be expanded by the end user by implementing new algorithms

Rosette Tracker [4]

Leaf

Java, ImageJ

Rosette type (Arabidopsis)

Projected rosette area, maximal diameter, stockiness, compactness, growth rate, temperature

RGB, IR, F

Open source, semi automated

Only tested on rosette type plant (Arabidopsis)

PlantCV [18]

Shoot, leaf

OpenCV, Python, NumPy and MatPlotlib

Setaria

Height, width, convex-hull, biomass and leaf area

RGB, F, NIR

Open source, semi automated

Computes details of the plant at only holistic level and not at individual component level. Hardware used to capture image - LemnaTec Scanalyzer\(^{3D-HT}\)

Leaf shApe deterMINAtion (LAMINA) [16]

leaf

Java, ImageJ

All leaf types

Leaf shape, area, quantify leaf serration, missing leaf area, indent width, depth.

RGB

Open source

Automated and semi-automated platform-independent software tool under license GNU GPL2. First open source tool for for quantification of leaf serration. Results are affected when leafs are non symmetrical in shape

Black spot [17]

Leaf

Python

All leaf types

Leaf area

RGB

Free software

Batch leaf processing, leaf imaged under flatbed scanner

LEAF GUI [20]

Leaf

Matlab

All leaf types

Leaf extension analysis-area state, vein state, areole state

RGB

Open source, semi automated

Destructive analysis

Circumnutation tracker [24]

Shoot

C++

Helianthus annuus

Circumnutation parameters: period, length, rate, shape, and clockwise- and counter-clockwise directions

Black/white or color time-lapse video images

Open source

Only tested on sunflower (Helianthus annuus)

Panicle TRAit phenotyping (P-Trap) [8]

Fruit

JAVA on Netbeans 7.3

Rice

Architecture of rice panicle, shape of seed, grain counting and detection

RGB

Opensource

Skeletonization process cannot accurately deal with curved panicle axes, and mislabel hair-like extensions on rice spikelets as branches

Leaf angle distribution toolbox [19]

Leaf

Matlab

Sugar beet

Leaf surface and leaf angle

RGB

Open source, semi automated

Requires stereo camera setup. Manual intervention for leaf segmentation for dense canopies

  1. Keys-RGB red–green–blue, IR infrared, NIR near infrared, F fluorescent