Code, tools, protocols

Confocal image of Arabidopsis root rotating. Nuclei are coloured purple to white.

FRETENATOR segmentation of an Arabidopsis root rotating. Segmented nuclei are multicoloured allowing individual nuclei to be discerned.

FRETENATOR segmentation of an Arabidopsis root rotating. Segmented nuclei are yellow at the top of the image and blue at the bottom

FRETENATOR2

Fiji plugins for segmentation, object classification, ratiometric analysis and intensiometric analysis. Includes a live updating GUI interface, a headless mode, a batch mode, object labelling, object classifier training and application and Trackmate 7 integration. This is under active development (as of 2026).

EZ-Peeler

EZ-Peeler is a top down surface segmentation tool that can be used to extract a non flat surface from a confocal stack. Data is exported as a segmented surface, a surface projection, an areamap and a heightmap.

Thermal image of Arabidopsis plants undergoing a humidity drop. Top view of a grid arrangement of blue plants turn purple, indicating they are getting colder as the humidity decreases.

Plant phenotyping equipment and protocols

Coming soon

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