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170 results for “Comparative Biology”
Data from: BioEncoder: a metric learning toolkit for comparative organismal biology
<p><strong>BioEncoder: a metric learning toolkit for comparative organismal biology</strong></p> <p><strong>Abstract </strong>- In the realm of biological image analysis, deep learning (DL) has become a core toolkit, e.g., for segmentation and classification. However, conventional DL methods are challenged by large biodiversity datasets characterized by unbalanced classes and hard-to-distinguish phenotypic differences between them. Here we present BioEncoder, a user-friendly toolkit for metric learning, which overcomes these challenges by focussing on learning relationships between individual data points rather than on the separability of classes. BioEncoder is released as a Python package, created for ease of use and flexibility across diverse datasets. It features taxon-agnostic data loaders, custom augmentation options, and simple hyperparameter adjustments through text-based configuration files. The toolkit's significance lies in its potential to unlock new research avenues in biological image analysis while democratizing access to advanced deep metric learning techniques. BioEncoder focuses on the urgent need for toolkits bridging the gap between complex DL pipelines and practical applications in biological research.</p> <p><strong>Dataset </strong>- This data repository includes two things: a snapshot of the BioEncoder package (BioEncoder-main.zip, version 1.0.0, downloaded from https://github.com/agporto/BioEncoder on 2024-07-19 at 17:20), and the damselfly dataset used for the case study presented in the paper (bioencoder_data.zip). The dataset archive also encompasses the configuration files and the final model checkpoints from the case study, as well as a script to reproduce the results and figures presented in the paper.</p> <p><strong>How to use - </strong>Get started by consulting the <a href="https://github.com/agporto/BioEncoder?tab=readme-ov-file#quickstart">GithHub repository</a> for information on how to install BioEncoder, then download the <a href="../records/10909614/files/BioEncoder-data.zip?download=1&preview=1">data archive</a> and run the script. Some parts of the script can be executed using the model checkpoints, for orther parts the training rountine needs to be run. </p>
The raw data of Souma, Katano, Doi et al. "Comparing environmental DNA with whole pond survey to estimate the total biomass of fish species in ponds" in Freshwater Biology
<p>The raw data of Souma, Katano, Doi, Takahara, and Minamoto. "Comparing environmental DNA with whole pond survey to estimate the total biomass of fish species in ponds" in Freshwater Biology.</p>
Fig. 4 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 4. Scytodid egg-sac. (A) Typical egg-sac of Scytodes cavernarum, S. fusca and the Philippines Scytodes sp. 2; and (B) Scytodes magna egg-sac. Note the denser silk surrounding the eggs of S. magna.
Fig. 8 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 8. Reproductive traits of five cave species of scytodids. (A) Mean (± S.E.) total number of spiderlings per female; (B) mean (± S.E.) egg hatching time (d); (C) mean (± S.E.) interval (d) between clutches; (D) mean (± S.E.) interval (d) between hatching and the next egg-sac production; (E) mean (± S.E.) number of clutches; and (F) mean (± S.E.) number of spiderlings per clutch. Different lower cases indicate significant differences.
Fig. 3 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 3. Maternal care of egg-sacs in spitting spiders. (A) Scytodes fusca female carrying her egg-sac in her chelicerae. (B) Guangxi Scyloxes sp. 1 female on the surface of the outer cave walls, staying close to her egg-sac. The egg-sac is suspended by two to three threads. (C) Web constructed by S. magna female. Her egg-sac is suspended by a few threads at the centre of the web.
Fig. 2 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 2. The 'cage within a cage' set-up for studying the natal dispersal patterns of scytodid spiders. Modified from Ruttan (1990).
Fig. 1 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 1. Four species of cave scytodid spiders. (A) female and (B) male Scytodes magna, body length = 10.5 mm; (C) female and (D) male S. fusca, body length = 5.8 mm; (E) female Philippines Scytodes sp. 2, body length = 5.6mm; and (F) female S. cavernarum, body length = 5.3 mm.
Fig. 6 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 6. Newly emerged Guangxi Scyloxes sp. 1 spiderlings spread out on the sparse silk nest, and female feeding on house fly alone. Body length of adult female = 11.5 mm.
Fig. 7 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 7. Relationship between the days in which spiderlings dispersed and spiderling mass in five cave scytodid species. (A) Scytodes fusca; (B) S. carvernarum; (C) Philippines Scytodes sp. 2.; (D) S. magna; and (E) Guangxi Scyloxes sp. 1.
Figure 1 in Comparative biology and growth rate of the two predatory mites, Cydnoseius negevi and Neoseiulus californicus (Acari: Phytoseiidae), reared on two pea cultivars
Figure 1. Age-specific fecundity (mx) and survivorship (lx) of Cydnoseius negevi and Neoseiulus californicus reared on two pea cultivars fed on nymphal stages of Tetranychus urticae at 27 ± 1°C.
Text-fig. 4. A – Alasia sp., pollen ornamentation, compared with B – extant Quercus castaneifolia C.A. Mey (courtesy of Natalia Naryshkina, Institute of Biology and Soil Science, Vladivostok), with similar verrucate – scabrate elements. Scale bar 1 µm. in In Situ Pollen Of Alasia, A Supposed Staminate Inflorescence Of Trochodendroides Plant
Text-fig. 4. A – Alasia sp., pollen ornamentation, compared with B – extant Quercus castaneifolia C.A. Mey (courtesy of Natalia Naryshkina, Institute of Biology and Soil Science, Vladivostok), with similar verrucate – scabrate elements. Scale bar 1 µm.
Figure 11 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 11. The efficacy of RM of orange peels against human pathogenic bacteria. ****Extremely significant among compared groups at p <0.05 level. Test 1: RM of Valen-cia orange; Test 2: RM of Mandarin orange; Test 3: RM of African navel orange.
Figure 6 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 6. The structure of bioactive compounds of RM of African Navel orange peel (1) Limonene; (2) Hexadecanoic acid, 2-hydroxy-1- (hydroxymethyl) ethyl; (3) 9,12-Octadecadienoic acid (Z,Z)-, methyl ester; (4) Terephthalic acid, di(2-ethylhexyl) ester; (5) α-Sitosterol; (6) α-D-Glucopyranose, 4-O-α-D-galactopyranosyl-; (7) 2-Methoxy-4-vinylphenol; (8) Eugenol; (9) cis-Vaccenic acid; (10) De-canal; (11) Vitamin E; (12) Dichloroxylenol.
Figure 3 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 3. GC-MS chromatogram of the RMs of orange peels. (A) RM of Valencia orange; (B) RM of Mandarin orange; (C) RM of African Navel orange.
Figure 2 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 2. The morphology of orange fruits. (A) Valenica orange; (B) Madarin orange; (C) African Navel orange.
Figure 5 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 5. The structure of bioactive compounds of RM of Mandarin orange peel (1) Lim-onene; (2) Octadecanoic acid, 2-hydroxy-1- (hydroxymethyl) ethyl; (3) Hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl; (4) Tetradecanamide; (5) n-Hexadecanoic acid; (6) α-D-Mannofuranoside, 1-O-(10-undecenyl)-; (7) 3-Deoxy-d-mannoic lactone; (8) Desulpho-sinigrin; (9) 2-Methoxy-4-vinylphenol; (10) Decanal; (11) Vitamin E; (12) 1-Monolinoleoylglycerol trimethylsilyl ether.
Figure 4 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 4. The structure of bioactive compounds of RM of Valencia orange peel (1) Limonene; (2) 9-Octadecenamide, (Z)-; (3) Hexadecanoic acid, 2- hy-droxy-1-(hydroxymethyl)ethyl; (4) Octadecanoic acid, 2-hydroxy-1-(hydroxymethyl)ethyl; (5) Tetradecanamide; (6) Hexadecanamide; (7) Ethyl iso-allocholate; (8) Ethyl α-d-glucopyranoside; (9) d-Glycero-d-galacto-heptose; (10) α-Sitosterol; (11) Vitamin E; (12) 4H-1-Benzopyran-4-one, 2-(3,4-dimethoxyphenyl)-5,6,7-trimethoxy-.
Figure 2 in Comparative population biology of Uca rapax (Smith, 1870) (Brachyura, Ocypodidae) from two subtropical mangrove habitats on the Brazilian coast
Figure 2. Uca rapax. Comparison of the median sizes of males and females at each site (A) and comparison of the median size of each sex and site (B). Boxes with at least one letter in common showed no statistically significant difference (P.0.05).
Figure 5 in Comparative population biology of Uca rapax (Smith, 1870) (Brachyura, Ocypodidae) from two subtropical mangrove habitats on the Brazilian coast
Figure 5. Uca rapax. Sex ratio by month (A) and size classes of carapace width (mm) (B) for populations from Itamambuca and Ubatumirim. Asterisks above the columns indicate significant differences between the proportions of males and females (P,0.05).
Figure 6 in Comparative population biology of Uca rapax (Smith, 1870) (Brachyura, Ocypodidae) from two subtropical mangrove habitats on the Brazilian coast
Figure 6. Uca rapax. Recruitment in the Itamambuca and Ubatumirim habitats by season of the year. Small letters above bars compare the proportions of juveniles among seasons in the same site. Bars with at least one letter in common did not differ statistically (P.0.05).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.