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opencc-zeroJan 2020View details →

IODP Expedition 361 Scanning electron microscope images

Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.

opencc-zeroMar 2020View details →

IODP Expedition 362 Scanning electron microscope images

opencc-by-4.0Nov 2020View details →

Scanning electron microscopy image dataset -- Abundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonian fjords and channels

Data set 1: E.huxleyi_morphotypes_Patagonia.zip Scanning electron microscopy images of Emiliania huxleyi cells found inhabit the southern Patagonia fjords during the late-spring 2015 and early-spring 2017.   Data set 2: E.huxleyi_abundances_Patagonia.zip Scanning electron microscope images of filters of plankton samples taken in 2015 and 2017 throughout southern Patagonia fjords. The "m" in sample name refer to the depth from which the sample was obtained.  Tables are provided to associate Emiliania huxleyi morphotypes' counts and taxonomic identifications to environmental variables from the samples for which data was used in statistical analysis.

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Data from: Setup in a clinical workflow and impact on radiotherapy routine of an in vivo dosimetry procedure with an electronic portal imaging device

High conformal techniques such as intensity-modulated radiation therapy and volumetric-modulated arc therapy are widely used in overloaded radiotherapy departments. In vivo dosimetric screening is essential in this environment to avoid important dosimetric errors. This work examines the feasibility of introducing in vivo dosimetry (IVD) checks in a radiotherapy routine. The causes of dosimetric disagreements between delivered and planned treatments were identified and corrected during the course of treatment. The efficiency of the corrections performed and the added workload needed for the entire procedure were evaluated. The IVD procedure was based on an electronic portal imaging device. A total of 3682 IVD tests were performed for 147 patients who underwent head and neck, abdomen, pelvis, breast, and thorax radiotherapy treatments. Two types of indices were evaluated and used to determine if the IVD tests were within tolerance levels: the ratio R between the reconstructed and planned isocentre doses and a transit dosimetry based on the γ-analysis of the electronic portal images. The causes of test outside tolerance level was investigated and corrected and IVD test was repeated during subsequent fraction. The time needed for each step of the IVD procedure was registered. Pelvis, abdomen, and head and neck treatments had 10% of tests out of tolerance whereas breast and thorax treatments accounted for up to 25%. The patient setup was the main cause of 90% of the IVD tests out of tolerance and the remaining 10% was due to patient morphological changes. An average time of 42 min per day was sufficient to monitor a daily workload of 60 patients in treatment. This work shows that IVD performed with an electronic portal imaging device is feasible in an overloaded department and enables the timely realignment of the treatment quality indices in order to achieve a patient's final treatment compliant with the one prescribed.

opencc-zeroDec 2017View details →

opencc-by-4.0Jan 2024View details →

Atlantic Meridional Transect (AMT) 14: scanning electron microscopy images of the coccolithophore community

Legacy scanning electron microscopy (SEM) images of plankton samples that were taken during Atlantic Meridional Transect cruise 14 (AMT 14), which sailed between the Faulkland Islands and the UK in 2004 (for more information see https://www.amt-uk.org/Cruises/AMT14 and the link to the cruise report therein). The SEM methodology applied to generate these images is described in Poulton et al. (2017) Coccolithophore ecology in the tropical and subtropical Atlantic Ocean: New perspectives from the Atlantic meridional transect (AMT) programme. Prog. Oceanogr. 158, 150–170 and follows Charalampopoulou et al. (2011) Irradiance and pH affect coccolithophore community composition on a transect between the North Sea and the Arctic Ocean. Mar. Ecol. Prog. Ser. 431, 25–43.  The 16 samples currently in this entry are from nine CTD stations of AMT14. There is a unique, compressed (.zip) file of SEM images for each sample (CTD station and water depth) with the following naming scheme:  AMT14_CTD#_A_WD, where CTD# denotes CTD number (e.g. CTD6), A denotes percentage of surface irradience level (e.g. 55 is 55% of surface irradience), and WD is water depth (m) of sample.    Each compressed sample folder contains ca. 600-700 SEM images in TIF file format. The name of each image relates to the date (day_month_image number) the image was taken on.    Correspondence should be directed to: Alex J. Poulton, Heriot-Watt University (a.poulton@hw.ac.uk) Please cite this compilation of SEM images in full (including doi) and acknowledge the Atlantic Meridional Transect programme if you are using these images: "AMT 14 was supported by the UK Natural Environment Research Council (NERC) through the Atlantic Meridional Transect consortium (NER/O/S/2001/00680)"   Associated publications: Poulton, A. J., Holligan, P. M., Charalampopoulou, A. & Adey, T. R. Coccolithophore ecology in the tropical and subtropical Atlantic Ocean: New perspectives from the Atlantic meridional transect (AMT) programme. Prog. Oceanogr. 158, 150–170 (2017). Sheward, R. M., Poulton, A.J., Young, J.R., de Vries, J., Monteiro, F.M. & Herrle, J.O. Cellular morphological trait dataset for extant coccolithophores from the Atlantic Ocean. Submitted to Scientific Data in Janurary 2024.

opencc-by-4.0Mar 2022View details →

Transmission electron microscopy (TEM) image datasets of peptide / protein nanowire morphologies

TEM image dataset containing four nanowire morphologies of bio-derived protein nanowires and synthetic peptide nanowires. The peptide / protein nanowires used in this study were synthesized and imaged by Brian Montz in Prof. Todd Emrick's research group at the Department of Polymer Science and Engineering Department, University of Massachusetts Amherst.  We acknowledge financial support from the U.S. National Science Foundation, Grant NSF DMREF #1921839 and DMREF #1921871. Nanowires were classified into either of the four morphologies: bundle, singular, dispersed or network. Each morphology contains 100 images (jpg files). For the dispersed and network morphologies, because these two morphologies are harder to visually distinguish, we have created manual segmentation labels of the nanowires (included in these two morphology folders as png files). Percolation analysis was done on these manually segmented nanowires to provide quantitative metric on whether the nanowires form a network in the image.  seg_mask_5_resolutions.zip contains ground truth 2D binary encoding of segmented nanowires at 5 resolutions. encoders_trained_with_optimized_hyperparameter.zip contains 4 sets of encoders trained with either SimCLR or Barlow-Twins self-supervised methods on either generic TEM images, or generic everyday photographic images (each with 5 replicates with different random seed) with optimized hyperparameters. Open-access datasets that have been used during self-supervised training. <ul> <li>2021-CEM500K.zip contains 10,000 images that was used as "generic TEM images" to train the encoders with self-supervised methods, these are a random selection from the CEM500k open-access dataset. DOI: <a href="https://doi.org/10.7554/eLife.65894">10.7554/eLife.65894</a></li> <li>2022-1000-ImageNet.zip contains 1,000 images from the ImageNet1k dataset, each come from a different category. DOI: <a href="http://doi.org/10.1007/s11263-015-0816-y">10.1007/s11263-015-0816-y</a></li> </ul> Open-access datasets that our machine learning workflow have been applied to: <ul> <li>2022-AutoDetect-mNP-morphology.zip contains a selected TEM images of nanoparticles categorized in 3 morphologies from the AutoDetect-mNP datasets: DOI: <a href="http://doi.org/10.6078/D1WT44">10.6078/D1WT44</a> and DOI: <a href="http://doi.org/10.6078/D1S12H">10.6078/D1S12H</a></li> <li>2021-TEM virus.zip contains TEM images of 9 types of viruses from the TEM virus dataset. Matuszewski, Damian; Sintorn, Ida-Maria (2021), “TEM virus dataset”, Mendeley Data, V3, DOI: <a href="http://doi.org/10.17632/x4dwwfwtw3.3">10.17632/x4dwwfwtw3.3</a></li> </ul> The official github page of the implementation of the machine learning models is <a href="https://github.com/arthijayaraman-lab/semi-supervised_learning_microscopy_images">semi-supervised_learning_microscopy_images</a>. If you use the dataset or the codes in the repository linked above, please cite the following <a href="https://doi.org/10.1039/D2DD00066K">manuscript</a>: S. Lu, B. Montz, T. Emrick and A. Jayaraman, Digital Discovery, 2022, 1, 816-833 , DOI: 10.1039/D2DD00066K

Figure 1 from: Parra-Gómez A, Pérez-Schultheiss J, Fernández LD (2024) Redescription of the enigmatic myriapod Hanseniella chilensis (Hansen, 1903) (Symphyla, Scutigerellidae) based on scanning electron microscope images of Chilean specimens. ZooKeys 1198: 1-15. https://doi.org/10.3897/zookeys.1198.119723

Figure 1 APG-17-a Male, dorsal view A head, first tergite and part of the second tergite (dfs-distinct frontal seta, ms-macroseta) B tergites 2–5 (am-anterolateral macrochaeta, hm-hind macrochaeta, pm-posterolateral macrochaeta) C tergites 11–13 D last tergite and cerci (hm-hind macrochaeta (abraded), hs-hind seta). Scale bars: 200.0 µm (A–C); 100.0 µm (D).

Figure 4 from: Parra-Gómez A, Pérez-Schultheiss J, Fernández LD (2024) Redescription of the enigmatic myriapod Hanseniella chilensis (Hansen, 1903) (Symphyla, Scutigerellidae) based on scanning electron microscope images of Chilean specimens. ZooKeys 1198: 1-15. https://doi.org/10.3897/zookeys.1198.119723

Figure 4 Illustrations showing some relevant structures of the species A antennomere 20 of a male B apical antennomere (sensory organs not as detailed as described due to their small size, smallest one not visible on this angle) C distal end of the first pair of legs D distal end of the last pair of legs (frontal seta abraded) E styli. Scale bar: 50 µm.

Figure 3 from: Parra-Gómez A, Pérez-Schultheiss J, Fernández LD (2024) Redescription of the enigmatic myriapod Hanseniella chilensis (Hansen, 1903) (Symphyla, Scutigerellidae) based on scanning electron microscope images of Chilean specimens. ZooKeys 1198: 1-15. https://doi.org/10.3897/zookeys.1198.119723

Figure 3 PG-71-L-a Female, ventral view A head and first pair of legs B ventral surface details proximal to left leg of pair 8 and its 2 first podomeres, podomere 4 and 5 of pair 7 partially show (lm-laminar needles, sc-scale-like cuticle, slm-"scales" with laminar needles) C coxal sac near leg pair 4 D last pair of legs and cerci (ap-apical seta, ls-large seta, os-outer seta). Scale bars: 100.0 µm (A, D); 50.0 µm (B); 20.0 µm (C).

Figure 2 from: Parra-Gómez A, Pérez-Schultheiss J, Fernández LD (2024) Redescription of the enigmatic myriapod Hanseniella chilensis (Hansen, 1903) (Symphyla, Scutigerellidae) based on scanning electron microscope images of Chilean specimens. ZooKeys 1198: 1-15. https://doi.org/10.3897/zookeys.1198.119723

Figure 2 Details of some relevant structures of APG-17-a Male (A, B) and PG-71-L-a Female (C, D) A central rod and triangular sulcus from the top of the head (hs-hind seta, oe-ovoid end, ss-short seta, ts-triangular sulcus) B tergal surface of tergite 3 (cr-cuticular rim) C Tömösváry organ and proximal surface (km-knob with microseta, lp-linguiform protuberance) D apical zone of the last antennomere (sb-sensilla basiconica, so-sensory organ). Scale bars: 50.0 µm (A, B); 10.0 µm (C, D).

Figure 5 from: Parra-Gómez A, Pérez-Schultheiss J, Fernández LD (2024) Redescription of the enigmatic myriapod Hanseniella chilensis (Hansen, 1903) (Symphyla, Scutigerellidae) based on scanning electron microscope images of Chilean specimens. ZooKeys 1198: 1-15. https://doi.org/10.3897/zookeys.1198.119723

Figure 5 All known records of Hanseniella chilensis (Hansen, 1903). Diamond = uncertain records from the literature, Star = new record herein, Circle = literature records.

opencc-zeroDec 2015View details →

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Data from: Reconstruction of genetically identified neurons imaged by serial-section electron microscopy

Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identified neurons, and developed a protocol that enhances the electron-density of the labeled cells and while retaining quality of the ultrastructure. The high contrast of the marked neurons enabled two innovations that dramatically speed data acquisition: targeted high-resolution reimaging of regions selected from rapidly-acquired lower resolution reconstruction, and an unsupervised segmentation algorithm. This pipeline reduces imaging and reconstruction times by at least two orders of magnitude, facilitating directed inquiry of circuit motifs.

opencc-zeroAug 2015View details →

IODP Expedition 351 Scanning electron microscope images

Text-fig. 39. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 3"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment, containing one kind of pollen; b, d, e) Pollen grains from stamen fragment in polar (b, d) and equatorial (e) views showing the long colpi with coarsely verrucate aperture membranes; note the semitectate-reticulate tectum in the mesocolpium regions and foveolate-punctate tectum in the polar regions and along the aperture margins; c) Detail of pollen wall showing smooth muri and short, densely-spaced columellae. Specimen, Catefica 49-S107785 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1.5 Μm (c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 39. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 3"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment, containing one kind of pollen; b, d, e) Pollen grains from stamen fragment in polar (b, d) and equatorial (e) views showing the long colpi with coarsely verrucate aperture membranes; note the semitectate-reticulate tectum in the mesocolpium regions and foveolate-punctate tectum in the polar regions and along the aperture margins; c) Detail of pollen wall showing smooth muri and short, densely-spaced columellae. Specimen, Catefica 49-S107785 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1.5 Μm (c).

Text-fig. 35. Scanning electron microscope (SEM, a, b, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, e) images of "Paisia-like follicle"; Catefica locality, Portugal. a) Lateral view of slender follicle with an almost straight ventral margin and a slightly curved dorsal margin; b) Lateral view of small, broad follicle with slightly sinuous ventral margin and rounded dorsal margin; c) Lateral view of small, broad follicle with slightly sinuous ventral margin and rounded dorsal margin; d) Apical part of follicle in (a) showing the slight apical cleft in the probable stigmatic region; e) Transverse section (orthoslice xy0407) of follicle showing ovules and distinct follicle wall with small, thin-walled cells of the outer epidermis (arrow), larger, isodiametric cells of the mesocarp and an inner layer of smaller, thin-walled cells. Specimens, Catefica 50-S171523 (a, d), Catefica 343-S171515 (b), Catefica 49-S174929 (c, e). Scale bars = 300 Μm (a–c), 100 Μm (d, e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 35. Scanning electron microscope (SEM, a, b, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, e) images of "Paisia-like follicle"; Catefica locality, Portugal. a) Lateral view of slender follicle with an almost straight ventral margin and a slightly curved dorsal margin; b) Lateral view of small, broad follicle with slightly sinuous ventral margin and rounded dorsal margin; c) Lateral view of small, broad follicle with slightly sinuous ventral margin and rounded dorsal margin; d) Apical part of follicle in (a) showing the slight apical cleft in the probable stigmatic region; e) Transverse section (orthoslice xy0407) of follicle showing ovules and distinct follicle wall with small, thin-walled cells of the outer epidermis (arrow), larger, isodiametric cells of the mesocarp and an inner layer of smaller, thin-walled cells. Specimens, Catefica 50-S171523 (a, d), Catefica 343-S171515 (b), Catefica 49-S174929 (c, e). Scale bars = 300 Μm (a–c), 100 Μm (d, e).

Text-fig. 16. Scanning electron microscope (SEM) images of "Stamen fragments with in situ Clavatipollenites- or Asteropollis-type pollen" (sp. 1: a–c; sp. 2: d–f; sp. 3: g–i); Catefica locality, Portugal. a) Stamen fragment showing pollen sacs; b) Distal view of pollen grain from (a) showing semitectate-reticulate tectum; c) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered, columellae supporting muri with fine pits and rounded supratectal ornamentation; note orbiculae with a finely spiny surface (arrows); d) Stamen showing very short filament, lateral pollen sacs and short apical extension of the narrow connective; e) Folded pollen grain from (d) showing semitectate-reticulate tectum; f) Detail of pollen wall from (d) showing the semitectatereticulate tectum and muri with fine rounded ornamentation; g) Stamen fragment; h, i) Detail of pollen grains from (g) showing the semitectate-reticulate tectum with smooth muri, long scattered columellae and tiny scattered orbicules (arrow). Specimens, Catefica 50-S170395 (a–c), Catefica 49-S172561 (d–f), Catefica 50-S170390 (g–i). Scale bars = 600 Μm (a, d, g), 6 Μm (b, e, h), 1.5 Μm (c, f, i). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 16. Scanning electron microscope (SEM) images of "Stamen fragments with in situ Clavatipollenites- or Asteropollis-type pollen" (sp. 1: a–c; sp. 2: d–f; sp. 3: g–i); Catefica locality, Portugal. a) Stamen fragment showing pollen sacs; b) Distal view of pollen grain from (a) showing semitectate-reticulate tectum; c) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered, columellae supporting muri with fine pits and rounded supratectal ornamentation; note orbiculae with a finely spiny surface (arrows); d) Stamen showing very short filament, lateral pollen sacs and short apical extension of the narrow connective; e) Folded pollen grain from (d) showing semitectate-reticulate tectum; f) Detail of pollen wall from (d) showing the semitectatereticulate tectum and muri with fine rounded ornamentation; g) Stamen fragment; h, i) Detail of pollen grains from (g) showing the semitectate-reticulate tectum with smooth muri, long scattered columellae and tiny scattered orbicules (arrow). Specimens, Catefica 50-S170395 (a–c), Catefica 49-S172561 (d–f), Catefica 50-S170390 (g–i). Scale bars = 600 Μm (a, d, g), 6 Μm (b, e, h), 1.5 Μm (c, f, i).

Text-fig. 15. Scanning electron microscope (SEM) images of stamen with "Asteropollis-type pollen sp. 2"; Catefica locality, Portugal. a) Stamen with pollen in situ showing the dome-shaped extension of the connective with hairs; b–d) Pollen in situ in stamen in (a) showing poorly defined pentachotomocolpate (b, d) and possibly tetrachotomocolpate (c) apertures and semitectate-reticulate tectum; e) Detail of broken pollen grains showing the loosely attached reticulum, long scattered columellae and thick foot layer. Specimen, Catefica 49-S101209 (a–e). Scale bars = 600 Μm (a), 6 Μm (b–e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 15. Scanning electron microscope (SEM) images of stamen with "Asteropollis-type pollen sp. 2"; Catefica locality, Portugal. a) Stamen with pollen in situ showing the dome-shaped extension of the connective with hairs; b–d) Pollen in situ in stamen in (a) showing poorly defined pentachotomocolpate (b, d) and possibly tetrachotomocolpate (c) apertures and semitectate-reticulate tectum; e) Detail of broken pollen grains showing the loosely attached reticulum, long scattered columellae and thick foot layer. Specimen, Catefica 49-S101209 (a–e). Scale bars = 600 Μm (a), 6 Μm (b–e).