Table 1.
State-of-the-art high throughput shoot phenotyping software tools
| 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 |
| 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 |
Keys-RGB red–green–blue, IR infrared, NIR near infrared, F fluorescent