PlantDieseaseDetection

demos/PlantDieseaseDetection.ipynb

@@ -0,0 +1,47 @@
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+    "# Plant disease\n",
+    "Sources:\n",
+    "- https://www.sciencedirect.com/science/article/abs/pii/S2352938521001361\n",
+    "- https://www.mdpi.com/2072-4292/14/23/5947\n",
+    "- https://link.springer.com/article/10.1007/s43154-020-00004-7/tables/1\n",
+    "<table>\n",
+    "<thead class=\"c-article-table-head\"><tr><th class=\"u-text-left \"><p>Disease</p></th><th class=\"u-text-left \"><p>Autonomous</p></th><th class=\"u-text-left \"><p>Material</p></th><th class=\"u-text-left \"><p>Platform description</p></th><th class=\"u-text-left \"><p>Spectral range</p></th><th class=\"u-text-left \"><p>Data processing</p></th><th class=\"u-text-left \"><p>References</p></th></tr></thead><tbody><tr><td rowspan=\"2\" class=\"u-text-left \"><p>Powdery mildew</p></td><td class=\"u-text-left \"><p>Yes (green house)</p></td><td class=\"u-text-left \"><p>Barley</p></td><td class=\"u-text-left \"><p>Spectral imaging with automated sensor positioning system inside the greenhouse</p></td><td class=\"u-text-left \"><p>VNIR (400–1000&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Simplex volume maximisation (SiVM) and support vector machine (SVM)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 21\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR21\" id=\"ref-link-section-d118707657e567\">21</a>••]</p></td></tr><tr><td class=\"u-text-left \"><p>No (laboratory conditions)</p></td><td class=\"u-text-left \"><p>Barley</p></td><td class=\"u-text-left \"><p>Imaging setup with translation stage for sample presentation</p></td><td class=\"u-text-left \"><p>VNIR (400–1000&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Linear discriminant analysis (LDA) and feature selection with ReliefF</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 25\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR25\" id=\"ref-link-section-d118707657e584\">25</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Grey mould leaf infection (<i>Botrytis cinerea</i>, fungi)</p></td><td class=\"u-text-left \"><p>Semi (indoor)</p></td><td class=\"u-text-left \"><p>Tomato</p></td><td class=\"u-text-left \"><p>Plant growth chamber with additional lightening to ensure uniform illumination</p></td><td class=\"u-text-left \"><p>5 bands: red, green, blue, near-infrared and red-edge</p></td><td class=\"u-text-left \"><p>Self-organising classifier to classify healthy and infected tissue</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 3\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR3\" id=\"ref-link-section-d118707657e607\">3</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Potato Y virus (<i>Potyviridae</i>, virus)</p></td><td class=\"u-text-left \"><p>Semi (field condition)</p></td><td class=\"u-text-left \"><p>Potato</p></td><td class=\"u-text-left \"><p>A tractor-mountable measurement box carrying spectral imager, protection from external lighting and embedded PC</p></td><td class=\"u-text-left \"><p>VNIR (400–1000&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Deep learning (fully convolutional neural network)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 10\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR10\" id=\"ref-link-section-d118707657e630\">10</a>•]</p></td></tr><tr><td class=\"u-text-left \"><p>Tulip break virus</p></td><td class=\"u-text-left \"><p>Semi (field condition)</p></td><td class=\"u-text-left \"><p>Tulip</p></td><td class=\"u-text-left \"><p>Field rail system with hand driven trolley platform</p></td><td class=\"u-text-left \"><p>RGB combined with NIR</p></td><td class=\"u-text-left \"><p>Deep learning (Faster R-convolutional neural network)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 9\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR9\" id=\"ref-link-section-d118707657e649\">9</a>•]</p></td></tr><tr><td class=\"u-text-left \"><p><i>Sclerotinia sclerotiorum</i> (fungi)</p></td><td class=\"u-text-left \"><p>No (laboratory conditions)</p></td><td class=\"u-text-left \"><p>Oilseed rape</p></td><td class=\"u-text-left \"><p>Indoor setup with translation stage used for imaging the plants</p></td><td class=\"u-text-left \"><p>VNIR (384–1034&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Partial least square discriminant analysis, SVM, radial basis function neural network, emerging learning neural network to detect disease</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 23\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR23\" id=\"ref-link-section-d118707657e671\">23</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Apple scab (<i>Venturia inaequalis</i>, fungus)</p></td><td class=\"u-text-left \"><p>No (laboratory conditions)</p></td><td class=\"u-text-left \"><p>Apple</p></td><td class=\"u-text-left \"><p>Indoor spectral imaging setup with translation stage for samples presentation</p></td><td class=\"u-text-left \"><p>SWIR (1000–2500&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Partial least square discriminant analysis (PLS-DA)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 22\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR22\" id=\"ref-link-section-d118707657e694\">22</a>]</p></td></tr><tr><td rowspan=\"2\" class=\"u-text-left \"><p>Anthracnose (<i>Colletotrichum</i>, fungi)</p></td><td class=\"u-text-left \"><p>Yes (field)</p></td><td class=\"u-text-left \"><p>Strawberry</p></td><td class=\"u-text-left \"><p>A mobile (4 wheels) platform with mounted spectral sensor (non-imaging)</p></td><td class=\"u-text-left \"><p>VNIR and SWIR (350–2500&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Vegetation indexes, step wise discriminant analysis (SDA), Fisher discriminant analysis (FDA), k-nearest neighbours (kNN)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 20\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR20\" id=\"ref-link-section-d118707657e717\">20</a>••]</p></td></tr><tr><td class=\"u-text-left \"><p>No (laboratory conditions)</p></td><td class=\"u-text-left \"><p>Strawberry</p></td><td class=\"u-text-left \"><p>Imaging setup with translation stage for sample presentation</p></td><td class=\"u-text-left \"><p>VNIR (400–1000&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Spectral angle mapper (SAM), SDA, correlation measure (CM), partial least square regression (PLSR)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 26\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR26\" id=\"ref-link-section-d118707657e734\">26</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Downy mildew (<i>Peronosporaceae</i>, fungi)</p></td><td class=\"u-text-left \"><p>Semi (green house)</p></td><td class=\"u-text-left \"><p>Grapevine</p></td><td class=\"u-text-left \"><p>Sensors and the light source arranged on a motorise line stage moving above the plants</p></td><td class=\"u-text-left \"><p>Two systems: non-imaging: (350–2500&nbsp;nm) and spectral imaging: (400–2500&nbsp;nm) and (940–2550&nbsp;nm)</p></td><td class=\"u-text-left \"><p>SAM + 3 downy mildew indices</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 27\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR27\" id=\"ref-link-section-d118707657e757\">27</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Early blight (<i>Alternaria solani</i>, fungi)</p></td><td class=\"u-text-left \"><p>No (laboratory conditions)</p></td><td class=\"u-text-left \"><p>Tomato</p></td><td class=\"u-text-left \"><p>Imaging setup with translation stage for sample presentation</p></td><td class=\"u-text-left \"><p>VNIR (380–1023&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Extreme learning machine (ELM) classifier model, successive projections algorithm (SPA)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 24\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR24\" id=\"ref-link-section-d118707657e780\">24</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Fire blight (<i>Erwinia amylovora</i>, bacteria)</p></td><td class=\"u-text-left \"><p>Semi (field condition)</p></td><td class=\"u-text-left \"><p>Apple</p></td><td class=\"u-text-left \"><p>Cameras mounted to an agricultural utility vehicle; an unmanned octocopter + multispectral camera</p></td><td class=\"u-text-left \"><p>RGB combined with infrared + non-imaging VNIR and SWIR (350–2500&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Vegetation indexes, PLSR and quadratic kernel support vector machine (QSVM)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 28\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR28\" id=\"ref-link-section-d118707657e804\">28</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Late blight (<i>Phytophthora infestans</i>, fungi)</p></td><td class=\"u-text-left \"><p>No (laboratory conditions)</p></td><td class=\"u-text-left \"><p>Tomato</p></td><td class=\"u-text-left \"><p>Imaging setup with translation stage for sample presentation</p></td><td class=\"u-text-left \"><p>VNIR (380–1023&nbsp;nm)</p></td><td class=\"u-text-left \"><p>Extreme learning machine (ELM) classifier model, successive projections algorithm (SPA)</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 24\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR24\" id=\"ref-link-section-d118707657e827\">24</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Mosaic virus (various genera, virus)</p></td><td class=\"u-text-left \"><p>No (laboratory condition)</p></td><td class=\"u-text-left \"><p>Cucumber</p></td><td class=\"u-text-left \"><p>Imaging setup with translation stage for sample presentation</p></td><td class=\"u-text-left \"><p>946&nbsp;nm to 2016&nbsp;nm</p></td><td class=\"u-text-left \"><p>PLS-DA, least square S-SVM</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 29\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR29\" id=\"ref-link-section-d118707657e846\">29</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Target and bacteria spots</p></td><td class=\"u-text-left \"><p>No (laboratory condition)</p></td><td class=\"u-text-left \"><p>Tomato</p></td><td class=\"u-text-left \"><p>Non-imaging spectrometer</p></td><td class=\"u-text-left \"><p>350–2500&nbsp;nm</p></td><td class=\"u-text-left \"><p>Vegetation indexes</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 30\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR30\" id=\"ref-link-section-d118707657e865\">30</a>]</p></td></tr><tr><td class=\"u-text-left \"><p>Cercospora leaf spot (<i>Cercospora beticola</i>)</p></td><td class=\"u-text-left \"><p>No (laboratory condition)</p></td><td class=\"u-text-left \"><p>Sugar beet</p></td><td class=\"u-text-left \"><p>Imaging setup with translation stage for sample presentation</p></td><td class=\"u-text-left \"><p>460–850&nbsp;nm</p></td><td class=\"u-text-left \"><p>Vegetation indexes and spherical k-means</p></td><td class=\"u-text-left \"><p>[<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 31\" title=\"\" href=\"/article/10.1007/s43154-020-00004-7#ref-CR31\" id=\"ref-link-section-d118707657e888\">31</a>]</p></td></tr></tbody>"
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