Hello Plant Biologists of Ecolog, A few months ago I sent out an email on ecolog to asses interest among the plant biologist community for an automated tool to phenotype stomatal traits. I received a positive response from many of you andit’s clear the community needs a tool to make stomatal phenotyping easier. Sven Eberhardt (Brown Uni.) and I have developed a tool to automatically count stomata and we have trained it on several hundred Balsam Poplar epidermal micrographs. The method appears to work very well for Balsam Poplars (machine v. human annotation has r2 = 0.92).
It’s clear that the training set needs to grow, and that’s why I’m reaching out to the plant biologists of ecolog. I’m searching for collaborators who can contribute several hundred high quality epidermal micrographs and then annotate them using the website we’ve developed. Here are the parameters that your images need to abide by:\ + The sample should come from populations within a species that encompasses a wide range of phenotypic variation. + Micrographs must be high quality, i.e. majority of image in focus, stomata clearly visible and unobstructed by epidermal features (e.g. trichomes). DIC images are the best. + Micrographs should be imaged at 20x or 40x. + Any preparation method is acceptable as long as it is a good prep. I am particularly interested in finding contributors for the following groups: Pinus, Oryza, Arabidopsis, Brachypodium, Maize, Populus, Medicago, and Mimulus. Collaborators will need to contribute and annotate several hundred (~200- 500) images in the next few weeks. In recognition of that effort you will be invited to join the project as a co-author, or acknowledged if you prefer. In addition to co-authorship/acknowledgement, contributors will have access to a beta version of the tool/website, and the method will perform very well on your particular preparation methodology and set of individuals. If you are interested in learning more, please email me and include a zip file of a representative sample of images. If you need to transfer large files, you can use UVM’s large file transfer service https://filetransfer.uvm.edu/. Thanks for the interest Ecolog & I can’t wait to see what’s out there. Sincerely, Karl Fetter Graduate Student Keller Lab Department of Plant Biology University of Vermont kfet...@uvm.edu
