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Data release for "OrchID: a Generalized Framework for Taxonomic Classification of Images Using Evolved Artificial Neural Networks"
<p><strong>Abstract</strong></p> <p>Taxonomic expertise for the identification of species is rare and costly. On-going advances in computer vision and machine learning have led to the development of numerous semi- and fully automated species identification systems. However, these systems are rarely agnostic to specific morphology, rarely can perform taxonomic “approximation” (by which we mean partial identification at least to higher taxonomic level if not to species), and frequently rely on costly scientific imaging technologies.</p> <p>We present a generic, hierarchical identification system for automated taxonomic approximation of organisms from images. We assessed the effectiveness of this system using photographs of slipper orchids (Cypripedioideae), for which we implemented image pre-processing, segmentation, and colour and shape feature extraction algorithms to obtain digital phenotypes for 116 species. The identification system trained on these digital phenotypes uses a nested hierarchy of artificial neural networks for pattern recognition and automated classification that mirrors the Linnean taxonomy, such that user-submitted photos can be assigned a genus, section, and species classification by traversing this hierarchy.</p> <p>Performance of the identification system varied depending on photo quality, number of species included for training, and desired taxonomic level for identification. High quality photos were scarce for some taxa and were under-represented in the training set, resulting in imbalanced network training. The image features used for training were sufficient to reliably identify photos to the correct genus but less so to the correct section and species.</p> <p>The outcomes of this project include a library of feature extraction algorithms called <em>ImgPheno</em>, a collection of scripts for neural network training called <em>NBClassify</em>, a library for evolutionary optimization of artificial neural network construction called <em>AI::FANN::Evolving</em> and a planned web application called <em>OrchID</em> for identification of user-submitted images. All project outcomes are open source and freely available.</p> <p><strong>About this release</strong></p> <p>This release corresponds belongs with our response to the reviewers of PLoS One. At this stage of the review cycle the manuscript is assessed as 'minor revision'. Consequently, we don't anticipate making more releases until publication.</p>
Fig 21. Primary types. A–F in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig 21. Primary types. A–F. Lectotypes (dorsal, labels). A–B. Ulomenes hypocrita Blanchard, 1850. C–D. Gastrohoplus mirabilis Moser, 1921. E–F. Schizochelus flavescens Blanchard, 1850. G–K. Syntype of Hercitis pygmaea Burmeister, 1855 (by Holger Dombrow). G. Dorsal. H. Lateral. I. Frontal. J. Posterior. K. Labels. Scale bars: A, C, E = 2 mm; G–J without scale (specimen about 4–4.2 mm according to original description).
Fig 19 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig 19. Lectotypes (dorsal, labels). A–B. Mallotarsus spadiceus Blanchard, 1850. C–D. Manodactylus gaujoni Moser, 1919. E–F. Manopus biguttatus Conte de Castelnau, 1840. G–H. Oedichira pachydactyla Burmeister, 1855. I–J. Amphicrania ursina Burmeister, 1855. K–L. Pectinosoma elongata Arrow, 1913. M–N. Aulanota sulcipennis Moser, 1924. O–P. Melolontha rufipennis Fabricius, 1801. Scale bars = 2 mm.
Fig 20 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig 20. Lectotypes (dorsal, labels). A–B. Pachycerus castaneipennis Guérin-Méneville, 1831. C–D. Anomalochilus singularis Blanchard, 1850. E–F. Demodema fallax Blanchard, 1850. G–H. Plectris tomentosa LePeletier de Saint-Fargeau & Audinet-Serville, 1828. I–J. Gama grandicornis Blanchard, 1850. K–L. Pachylotoma viridis Blanchard, 1850. M–N. Serica marmorea Guérin-Méneville, 1831. O–P. Rhinaspoides aeneofusca Moser, 1919. Scale bars = 2 mm.
Fig 17 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig 17. Lectotypes (dorsal, labels). A–B. Agaocnemis pruina Moser, 1918. C–D. Corminus canescens Burmeister, 1855. E–F. Anomalonyx uruguayensis Moser, 1921. G–H. Barybas nana Blanchard, 1850. I–J. Ctilocephala pelluscens Burmeister, 1855. K–L. Pseudohercitis viridiaenea Moser, 1921. M–N. Barybas volvulus Burmeister, 1855. O–P. Calodactylus tibialis Blanchard, 1850. Scale bars = 2 mm.
Fig. 14. A, D in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 14. A, D. Male habitus, lateral (without some appendages). B–C, F–G. Female abdomen detail (lateral, posterior). E. Male abdomen detail, ventral. H–I. Aedeagus (lateral, parameres apex). A–C. Ancistrosoma klugii Curtis, 1835. D–I. Pectinosoma elongata Arrow, 1913.
Fig. 16. Schizochelus Blanchard, 1850. A–C. Male abdomen, lateroventral. D. Female abdomen, lateral. E–F in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 16. Schizochelus Blanchard, 1850. A–C. Male abdomen, lateroventral. D. Female abdomen, lateral. E–F. Aedeagus (lateral, parameres apex). G–L. Protibia−tarsus (male, female) (with detail of tarsus: I = dorsal view; K = ventral view). A, E−H. Schizochelus flavescens Blanchard, 1850. B, I–J. Schizochelus bicoloripes Blanchard, 1850. C–D, K–L. Schizochelus mirabilis (Moser, 1921) comb. nov. Scale bars = 1 mm.
Fig 18 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig 18. Lectotypes (dorsal, labels). A–B. Ceraspis pruinosa LePeletier de Saint-Fargeau & Audinet- Serville, 1828. C–D. Ceratolontha venezuelae Arrow, 1948. E–F. Chariodactylus chacoensis Moser, 1919. G–H. Philochlaenia virescens Blanchard, 1842. I–J. Clavipalpus dejeani Laporte, 1832. K–L. Ctenotis obesa Burmeister, 1855. M–N. Euryaspis gaudichaudii Blanchard, 1850. O–P. Faula cornuta Blanchard, 1850. Scale bars = 2 mm.
Fig. 11 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 11. ♂♂. A−C. Head–prothorax dorsal, tarsus rotated laterally to apex. D−G. Aedeagus (lateral, parameres apex). H. Head−prothorax, ventral. A, D−E. Chariodactylus chacoensis Moser, 1919. B, F−H. Manodactylus gaujoni Moser, 1919. C. Macrodactylus pumilio Burmeister, 1855. Scale bars = 1 mm.
Fig. 10. A−B, D−F in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 10. A−B, D−F. Head−pronotum, dorsal. C. Head−prothorax, lateroventral. G. Metatibia, internal. A. ♀. B−G. ♂. H−K. Aedeagus (lateral, parameres apex). A−C, H−I. Ceratolontha venezuelae Arrow, 1948. D. Rhinaspis aenea Billberg, 1820. E. Rhinaspis ohausi Moser, 1921. F−G, J−K. Rhinaspis aeneofusca Moser, 1919. Scale bars = 1 mm.
Fig. 8. A−E. Pronotum−scutellum contact. F. Protibia. A. Ancistrosoma klugii Curtis, 1835. B. Chariodema virescens Blanchard, 1842. C in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 8. A−E. Pronotum−scutellum contact. F. Protibia. A. Ancistrosoma klugii Curtis, 1835. B. Chariodema virescens Blanchard, 1842. C. Ceraspis bivulnerata (Germar, 1824). D. Faula cornuta Blanchard, 1850. E−F. Manopus biguttata Conte de Castelnau, 1840. Scale bars = 1 mm.
Fig. 2 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 2. ♂♂. A–D. Head–prothorax dorsal, tarsus rotated laterally to apex. E–G. Metatibia. H–I. Aedeagus (lateral, parameres apex). A, E. Agaocnemis pruina Moser, 1918. B, F, H–I. Byrasba volvula (Burmeister, 1855). C, G. Hamatoplectris caracana Frey, 1969. D. Hieritis macrocera Burmeister, 1855. Scale bars = 1 mm.
Fig. 5. Barybas Blanchard, 1850. A–B in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 5. Barybas Blanchard, 1850. A–B. Head–prothorax dorsal, tarsus rotated laterally to apex. C–H. Male head (lateral, frontal), line = prothorax limit. I–J. Aedeagus (lateral, parameres apex). A, C–D. Barybas nana Blanchard, 1850. B, G–J. Barybas viridiaenea Moser, 1921. E–F. Barybas pellucens Burmeister, 1855. Scale bars = 1 mm.
Fig. 7. Calodactylus tibialis Blanchard, 1850. A in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 7. Calodactylus tibialis Blanchard, 1850. A. Male habitus, lateral (without some appendages). B. Male abdomen lateroventral detail. C–D. Aedeagus (lateral, parameres apex). E. Metatibia. Scale bars = 1 mm.
Fig. 6 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 6. ♂♂. A–D. Head (dorsal, ventral). E–F. Aedeagus (lateral, parameres apex). G–H. Mesoalinotum. A–B, E–F. Clavipalpus dejeani Laporte, 1832. C–D. Paulosawaya ursina (Blanchard, 1850) comb. nov. G. Barybas nana Blanchard, 1850. H. Macrodactylus pumilio Burmeister, 1855. a = scutum transverse carina; b = scutum–scutellum limit angulate. Scale bars = 1 mm.
Fig. 3. Alvarinus canescens Burmeister, 1855 in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 3. Alvarinus canescens Burmeister, 1855, ♂. A. Habitus, lateral (without some appendages). B. Head–prothorax dorsal, tarsus rotated laterally to apex. C. Metafemur. D–E. Aedeagus (lateral, parameres apex). Scale bars = 1 mm.
Fig. 4. A–C. Male metatarsus. D. Female metatarsus. E–H in Macrodactylini (Coleoptera, Scarabaeidae, Melolonthinae): primary types of type species and taxonomic changes to the generic classification
Fig. 4. A–C. Male metatarsus. D. Female metatarsus. E–H. Aedeagus (lateral, parameres apex). I–J. Antenna (♂, ♀). A. Plectris tomentosa LePeletier de Saint-Fargeau & Audinet-Serville, 1828. B, E–F. Anomonyx uruguayensis Moser, 1921. C–D, G–J. Oedichira pachydactyla Burmeister, 1855. Scale bars = 1 mm.
Figs 98-106 in Classification, Natural History, and Evolution of the Subfamily Peloniinae O (Coleoptera: Cleroidea: Cleridae). Part IX. Taxonomic revision of the New World genus Muisca S
Figs 98-106: Phalli. (98) Muisca dilatata. (99) M. insigna. (100) M. apicalis. (101) M. dozieri. (102) M. irrorata. (103) M. hirtula. (104) M. togata. (105) M. xanthura. (106) M. fera.
Figs 82-83 in Classification, Natural History, and Evolution of the Subfamily Peloniinae O (Coleoptera: Cleroidea: Cleridae). Part IX. Taxonomic revision of the New World genus Muisca S
Figs 82-83: Various organs. (82) M. octonotata, head, ventral view. (83) M. octonotata, forebody, ventral view.
Figs 2-13 in Classification, Natural History, and Evolution of the Subfamily Peloniinae O (Coleoptera: Cleroidea: Cleridae). Part IX. Taxonomic revision of the New World genus Muisca S
Figs 2-13: Various structures of Muisca testacea. (2) Head, frontal view. (3) Head, ventral view. (4) Head, dorsal view. (5) Prothorax, ventral view. (6) Antenna, male. (7) Spicular fork. (8) Maxilla. (9) Labrum. (10) Metendosternite. (11) Mandible. (12) Labium. (13) Metathoracic wing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.