Software and Tools

Plant Phenotyping Tools

iDIEL Plant software and image capture system design.


from Dobsrecu A, Scorza L, Tsaftaris S, McCormick AJ. 2017. A "Do-It-Yourself" phenotyping system: measuring growth and morphology throughout the diel cycle in rosette shaped plants. Plant Methods 13: 95. (Software source code and datasets available).

PS-Plant software.

Photomeric stereo training data set with annontated leaf masks.


Photomeric stereo test data set.

from Bernotas G, Scorza LCT et al.  (2019): Supporting data for "A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth." Supplementary files and software protocol can be download here here. GigaScience Database:


Cyanobacterial Synthetic Biology Tools


The CyanoGate toolkit (Kit #1000000146) (still coming online).

Most CyanoGate plasmids available here.

(from Vasudevan R, Gale GAR,  Schiavon AR, Puzorjov A, et al.) "CyanoGate: A Golden Gate modular cloning suite for engineering cyanobacteria based on the plant MoClo syntax" (Plant Physiology, doi:10.1104/pp.18.01401).


(from Gale GAR,  Schiavon AR, Puzorjov A, et al.) "Modification of cyanobacteria by conjugation using the CyanoGate modular cloning toolkit" (Journal of Visualized Experiments 152: e60451).