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<!DOCTYPE html>
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<h1>Software</h1>
<p>For my research I rely greatly on a wide range of software and image analysis tools developed by computer specialists. Using these greatly increase throughput, accuracy and reproducibility in plant phenotyping. Below I provide links to all of the software I commonly use and how I use them. Before embarking on a project I strongly recommend checking out <a href="https://quantitative-plant.org" target="_blank">quantitative-plant.org</a> as it is a central resource maintained by <a href="https://twitter.com/guillaumelobet/" target="_blank">@guillaumelobet</a> for available software and datasets.</p>
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<p><b>RhizoVision Explorer</b> Root image analysis software for quantification of disconnected or connected root systems.<br>
<a href="https://doi.org/10.1093/aobpla/plab056">FREE DOWNLOAD</a><br>
<a href="https://doi.org/10.1093/aobpla/plab056"><img alt="RhizoVisionExplorer" class="image fit" src="images/rhizovisionexplorer.png"></a></p>
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<p><b>ORS Dragonfly</b> Image analysis software with deep learning for analysing data collected from X-ray CT.<br>
<a href="https://www.theobjects.com/dragonfly">Academic/Non-profit license</a><br>
<a href="https://www.theobjects.com/dragonfly"><img alt="ORS Dragonfly" class="image fit" src="images/orsdragonfly.png"></a></p>
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<p><b>RootPainter</b> Image analysis software with deep learning for analysing Rhizotron images.<br>
<a href="https://doi.org/10.1111/nph.18387">FREE DOWNLOAD</a><br>
<a href="https://doi.org/10.1111/nph.18387"><img alt="RootPainter" class="image fit" src="images/rootpainter.png"></a></p>
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<p><b>FieldImageR</b> Image analysis scripts for analysing drone images.<br>
<a href="https://doi.org/10.1002/ppj2.20005">FREE DOWNLOAD</a><br>
<a href="https://doi.org/10.1002/ppj2.20005"><img alt="FieldImageR" class="image fit" src="images/fieldimager.png"></a></p>
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<p><b>PRIMAL</b> Machine learning pipeline (Random Forest) bundled into a R Shiny app for root system architecture.<br>
<a href="https://plantmodelling.github.io/primal/">FREE DOWNLOAD</a><br>
<a href="https://plantmodelling.github.io/primal/"><img alt="PRIMAL" class="image fit" src="images/primal.png"></a></p>
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<p><b>RootNav</b> Semi-automatic software for quantification of 2D root system architecture. I have used RootNav for processing multiple mapping populations grown on hydroponic pouches. This approach is particularly useful for root angle determination. Also check out RootNav 2.0 deep learning version.<br>
<a href="https://www.nottingham.ac.uk/research/groups/cvl/software/rootnav.aspx">FREE DOWNLOAD</a><br>
<a href="https://www.nottingham.ac.uk/research/groups/cvl/software/rootnav.aspx"><img alt="RootNav" class="image fit" src="images/rootnav.png"></a></p>
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<p><b>CellSeT</b> Semi-automatic software for quantifying root anatomy by segmenting out plant cells and assigning cell classes.<br>
<a href="https://www.nottingham.ac.uk/research/groups/cvl/software/cellset.aspx">FREE DOWNLOAD</a><br>
<a href="https://www.nottingham.ac.uk/research/groups/cvl/software/cellset.aspx"><img alt="CellSet" class="image fit" src="images/cellset.png"></a></p>
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<p><b>RooTrak</b> 3D Root segmentation software for X-ray Micro Computed Tomography (µCT) scanned plants.<br>
<a href="https://www.nottingham.ac.uk/research/groups/cvl/software/rootrak.aspx">FREE DOWNLOAD</a><br>
<a href="https://www.nottingham.ac.uk/research/groups/cvl/software/rootrak.aspx"><img alt="RooTrak" class="image fit" src="images/rootrak.png"></a></p>
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<p><b>RooTh</b> 3D Root skeletonisation and root system quantification software for X-ray Micro Computed Tomography (µCT) scanned plants.<br>
<a href="https://github.com/rootth/rooth">FREE DOWNLOAD</a><br>
<a href="https://github.com/rootth/rooth"><img alt="RooTh" class="image fit" src="images/rooth.png"></a></p>
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<section>
<p><b>OpenSimRoot</b> 3D Root simulation software that can integrate X-ray Micro Computed Tomography (µCT) & MRI scanned plants.<br>
<a href="https://rootmodels.gitlab.io">FREE DOWNLOAD</a><br>
<a href="https://rootmodels.gitlab.io"><img alt="OpenSimRoot" class="image fit" src="images/opensimroot.png"></a></p>
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<p><b>Fiji is just imageJ</b> Fiji is an image processing package, basically imageJ bundled with a lot of plugins which facilitate scientific image analysis. I personally use it to batch transform images (eg. crop, colour threshold) using the macro feature. There are many applications including measuring, skeletonisation and adding scale bars to images.<br>
<a href="https://fiji.sc">FREE DOWNLOAD</a><br>
<a href="https://fiji.sc"><img alt="Fiji" class="img-fluid" src="images/96px-Fiji-icon.png"></a></p>
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<p><b>OpenCV/PlantCV</b> Fiji may be a good starting point for image analysis but I have since transitioned to OpenCV and PlantCV functions with Jupyter notebooks.<br>
<a href="https://plantcv.org">FREE DOWNLOAD</a><br>
<a href="https://plantcv.sc"><img alt="PlantCV" class="img-fluid" src="images/96px-PlantCV-icon.png"></a></p>
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<p><b>RStudio</b> Statistics program for data processing and graphing. RStudio makes R easier to use. Notable packages inlcude "tidyverse" and "qtl". See My Code for my R code repository.<br>
<a href="https://www.rstudio.com">FREE DOWNLOAD</a><br>
<a href="https://www.rstudio.com"><img alt="RStudio" class="img-fluid" src="images/RStudio-Logo-Flat.png"></a></p>
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<p><b>Lab Mate - Molarity & Dilution</b> This is a simple molarity and dilution universal app that I made for iPhone, iPad and macOS. Feel free to contact me for a code.<br>
<a href="https://apps.apple.com/us/app/lab-mate-molarity-dilution/id1493317050?itsct=apps_box&itscg=30200"><img alt="Lab Mate Molarity Dilution app iPhone iPad Mac iOS" class="img-fluid" src="images/lab-mate-molarity-dilution.png" width="300"></a></p>
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