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FIGURE 4 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 4. Close-up RTIViewer snapshots of the region dorsal to the dorsal vertebral column on the main slab, taken under different lighting conditions but all processed using the specular enhancement mode (except for Figure 4A). Scale bar for all illustrations equals 10 mm. Comment on the settings in the RTIViewer software as visualised in the figures. A green sphere symbolises the direction of the incident light (upper right corner), a text box in the upper image margin contains the respective x- and ycoordinates of the incident light direction (the first value contains the x-coordinate, while the second one contains the ycoordinate), the zoom factor is given in brackets. A second text box contains the individual values of the specular enhancement mode (lower left corner). The first value stands for the parameter "specularity", the second one indicates the parameter "highlight size". The line drawings were sometimes made based on several RTI images with different settings to illustrate an individual impression more clearly. As far as the figures themselves are concerned, the interpretative drawings have tried to come as close as possible to the appearance and arrangement of the structures observed in the RTIViewer. However, some drawings, such as Figure 4B, represent rather idealised illustrations of the general pattern and arrangement of individual pycnofibre impressions in a given area. For this reason, the interpretative drawings may differ in detail from the respective RTI images to which they refer. In all figures, the orientation of the pycnofibres is marked by red arrows; the whitish semicircular indent, the starting point of most of the pycnofibres in the caudal region of the dorsal vertebrae, is symbolised by a red arc throughout Figure 4 and 5, the single occurrence of Type 2 pycnofibres is circled in red in the aforementioned figures. 4A. Overview of the pycnofibre impressions in the area dorsal to the dorsal vertebral column associated with the whitish amorphous rock surface under normal light. 4B. Interpretative drawing of Figure 4A (dorsal ribs in the lower right corner of the image) under normal light, idealised to give an overview of the spatial orientation of the pycnofibre impressions and therefore not reflecting the exact path of individual impressions. Thicker lines indicate better observable impressions. 4C. The same area as in 4A, seen under the specular enhancement mode. 4D. Pycnofibres of the caudalmost part of the area dorsal to the dorsal vertebral column (lower right corner). Note the pycnofibres showing a distinctive cross-over (red circle in 4D and 4E), representing Type 2. 4E. The same area as in 4D under other lighting conditions to highlight the overlapping impressions.
FIGURE 1 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 1. Images from the original publication by Georg August Goldfuss (1831). Main slab (1A) and counter slab (1B) of the holotype of Scaphognathus crassirostris IGPB Goldfuss 1304a (main slab) and 1304b (counter slab). 1C, Skeletal reconstruction of Scaphognathus crassirostris, including palaeobiological life reconstruction of two Scaphognathus crassirostris specimens in their presumed marginal marine habitat. However, the skeletal reconstruction contains two major errors: firstly, four instead of three clawed fingers are to be seen on the hand, and secondly, the long tail characteristic of most non-pterodactyloid pterosaurs is missing.
FIGURE 13 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 13. Different areas on the main slab as well as on the counter slab sum up the general mode of the soft part preservation in the Scaphognathus crassirostris holotype IGPB Goldfuss 1304b. The impressions on the main slab (images on the left figure side; 13A, 13C, and 13E) are in accordance with the corresponding elevations of the same impressions on the counter slab (right images 13B, 13D, and 13F; see for a direct comparison the red arrows). This illustrates the observation made by Goldfuss (1831), who stated that on the main slab, the soft part impressions are to be seen as grooves, whereas on the counter slab, they are shaped as elevations. This observation led Goldfuss (1831, p. 108) to the conclusion that the pycnofibres must have originally been under the limestone layer of the counter slab. 13A-13B. Pycnofibre impressions and the remains of the wing membrane including the aktinofibrils close to the articulation of the first with the second phalanx of the right wing finger (putative patagium border marked in both images by a red transversal line). 13C-13D. The impressions between the deltopectoral crest of the humerus and the zeugopodial bones of the right wing. Note the strong contrast between the deeply embedded grooves on the main slab (13C) and the clearly perceptible elevations on the counter slab (13D). 13E-13F. Blood vessel impressions. The grooves of the blood vessels on the main slab trace the exact contour of the corresponding elevations on the counter slab.
FIGURE 11 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 11. Close-up RTIViewer snapshots of the region enclosed by the articulation of the humerus with the zeugopodial bones of the right wing and the deltopectoral crest of the humerus on the counter slab, taken under different lighting conditions, but all processed using the specular enhancement mode (except 11A and 11E). Scale bar for all illustrations equals 10 mm. Markings for various soft part impressions used throughout this Figure: red lines illustrate the path of the impressions and their orientation to each other and a red ellipse marks the longest blood vessel. 11A. The geometrically organised soft parts ventral to the deltopectoral crest of the humerus (uppermost left corner) and the zeugopodial bones of the right wing (lower margin). Note the distinct crossing of the two thick main branches (red circle in 11A and 11B). The arrangement of these impressions of a soft tissue type that cannot be determined with absolute certainty, but very probably once belonging to the Patagium reminds of the arrangement of the main vessels in the complex vessel system in the Rhamphorhynchus specimen JME SOS 4784 (Tischlinger and Frey, 2002; Frey et al., 2003). In this specimen, a large main vessel serves as an attachment point for side channels branching off from it at more or less right angles. 11B. Interpretative drawing of 11A. 11C-11D. Specular enhancement images of Figure 11A under different lighting conditions. The soft part impressions likely representing former patagium vessels appear either as elevations (11C) or as grooves (11D). The parallel arrangement of some side branches is confirmed under all lighting conditions, suggesting its interpretation as part of the patagium. 11E. The longest, unbranched and strongly bifurcated blood vessel (red circle in 11E). 11F-11G. The appearance of the pit-like depressions already shown in Figure 10 associated with the blood vessels.
FIGURE 7 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 7. Close-ups of RTIViewer snapshots of the region ventral to the zeugopodial bones of the right wing on the main slab, taken under different lighting conditions, but all processed using the specular enhancement mode (except for 7D and 7G). Scale bar for all illustrations equals 10 mm, except for Figure 7A (1 mm). Markings for various pycnofibre types used throughout this figure: red circle illustrating Type 5 (the tuft); red arrows highlighting the main branch and several side branches of Type 6 (feather-like) as well as the individual path of single pycnofibre impressions at the lower margin of the main slab (Fig. 7C). For better comparability, the outermost (longest) side branches of the "feather" are highlighted by red markings (inclusive all terminal bifurcations). 7A. Type 5 pycnofibre. Some impressions suggest a connection between the Type 5 and 6 pycnofibres, but are not consistent in their appearance. 7B. Schematic drawing of Figure 7A, showing possible connections between the tuft and neighbouring grooves (see red arrows, although not entirely confirmable by the RTI images). 7C. The accumulation of Type 1 pycnofibres at the edge of the main slab near the articulation of the first with the second phalanx of the right wing finger (towards the lower right corner). Red arrows indicate the opposing directions of the impressions. Note in the upper right image corner the sixth pycnofibre type of Figure 7D-7I (green circle). 7D. Type 6 pycnofibre, dorsal to the articulation of the first with the second phalanx of the right wing finger (lower right image corner). Some side branches bear even smaller ones (red parabola-like upside-down markings in Figure 7D, 7E and 7H). 7E. Specular enhancement image of the sixth type. 7F. Interpretative sketch of 7E, highlighting the similarity with a feather as Goldfuss (1831) previously pointed out. The extent, length and number of several side branches are difficult to determine. Therefore, the drawing may differ in some details from the structure visible in the RTI images.7G-7H. The feather-like pycnofibre impression from a greater distance under normal light (7G) and processed by using the specular enhancement mode (7H). 7I. Sketch of Figure 7G and 7H, suggesting no real connection between the Type 5 (tuft) and Type 6 (feather) pycnofibres.
FIGURE 3 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 3. Close-ups of two different regions on the main slab demonstrating the optical difference between unprepared regions associated with soft parts (green arrow) and the surfaces prepared by Goldfuss (red arrow), without being processed with the specular enhancement mode. 3A. The sharp border between the unprepared ochre- and beige-coloured limestone surface and the homogenous, striated surface directly ventral to the above-mentioned bones, which underwent preparation. 3B. The striations created by Goldfuss are more clearly discernible dorsal to the cervical vertebral column (red arrow). Scale bar in both illustrations equals 10 mm.
FIGURE 6 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 6. Close-ups of RTIViewer snapshots of the region ventral to the zeugopodial bones of the right wing on the main slab, taken under different lighting conditions, but all processed using the specular enhancement mode (except for 6A and 6H). Scale bar for all illustrations equals 10 mm, except for 6G and 6H (one millimetre). Markings for various pycnofibre types used throughout this Figure: Type 2 (bifurcated; yellow circle), Type 3 (trident-like; orange circle), Type 5 (tuft, red circle), and Type 6 (symmetrical "feather", green circle). The path of individual pycnofibre impressions, and the path of individual side branches of single impressions are illustrated by red markings (either by straight lines or by curved arcs as in 6D, 6E, and 6H). 6A, 6C. Overview of the area with the pycnofibres ventral to the zeugopodial bones of the right wing (upper left corner of both images) and the phalanges of the right wing finger (near the right image margin) under normal light (6A) as well as under the specular enhancement mode (6C). 6B. Schematic sketch of Figure 6C, showing the appearance of the pycnofibre impressions under normal light. 6D-6E. Closeups of 6C. Note the parallel to subparallel alignment of several pycnofibre impressions (red vertical lines in 6D and 6E) and the easily detected caudally curved side branches of the Type 4 pycnofibre (red rectangle in 6F). The complex structure with several putative side branches at the right image margin between Type 2 and 3 pycnofibres (red arrow) is more likely to represent an arrangement of overlapping impressions of individual pycnofibres. 6F. Sketch of the RTI images 6D and 6E. 6G. Detailed close-up of the Type 2 pycnofibre, outlined by red markings. 6H. Detailed close-up of the Type 5 pycnofibre. The longest branch in the middle has a distinctive bifurcation (red circle).
FIGURE 10 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 10. Close-up RTIViewer snapshots of the region enclosed by the articulation of the humerus with the zeugopodial bones of the right wing and the intersection point of the zeugopodial bones of both wings on the main slab, taken under different lighting conditions, but all processed using the specular enhancement mode (with the exception of 10A and 10B). Scale bar for all illustrations equals 10 mm. Markings for various soft part impressions used throughout this Figure: the longest soft part impression connecting the zeugopodial bones of the right wing with the humerus of the same wing is marked by a thick transversal red line, the other shorter ones running parallel to subparallel to each other by thin red lines, channel-like grooves on the bone surface are pointed out by a red rectangle. Dissolved limestone layer surfaces are pointed out by red rectangles. 10A. Overview over the area with the organic remains between the zeugopodial bones of both wings. The location of the most pronounced grooves is highlighted (yellow rectangle) as well as the blood vessels (orange rectangle). Image modified from the.rti file of Jäger et al. (2018). 10B. The impressions in this area do not share a common starting point. Note the parallel to subparallel arrangement of the shorter soft part impressions. Also, pay attention to the channel-like grooves on the bone surface and the whitish irregularly-shaped stains of the sediment layer between the zeugopodial bones, probably being the result of aqueous solutions, which might have occurred during fossilisation, and which might have dissolved the former uppermost sedimentary layer. Although speculative, such solutions might have been derived from escaping body fluids in the context of the taphonomy of the integumentary appendages (see Foth, 2012 for a detailed discussion). 10C-10D. Specular enhancement images of 10B, taken under different lighting conditions to highlight the parallel arrangement of the soft part-related impressions and the channel-like grooves on the bones. Note the oblong channel connecting individual shorter ones (thick green arrow) and especially the zigzag pattern of some shorter channels (brown ellipse in both figures). 10E. Interpretative drawing of Figure 10C and 10D. 10F. The blood vessels near the intersection point of the zeugopodial bones of both wings. The subparallel alignment of the vessels (red slightly curved lines in Figure 10F) might indicate a similarity with the blood vessel system in the Rhamphorhynchus specimen JME SOS 4784 (Tischlinger and Frey, 2002; Frey et al., 2003). Note the distinct bifurcation of the rightmost vessel (red circle). Image modified from the.rti file of Jäger et al. (2018). 10G. Detailed close-up of Figure 10F. Small pits (red circles) might be the result of degradation processes in the context of the decay of the pterosaur carcass, although the exact generic process is uncertain.
FIGURE 9 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 9. Close-ups of RTIViewer snapshots of the region ventral to the cervical vertebral column and at the articulation of the first with the second phalanx of the right wing finger on the main slab, processed without (9A and 9D) and with the specular enhancement mode (9B and 9E). Scale bar for all illustrations equals 10 mm. Markings for various pycnofibre types used throughout this Figure: The Type 2 (bifurcated) pycnofibre type is marked by a red rectangle, orange-brown sediment surfaces on which the aktinofibrils impressions are to be found are illustrated by a red rectangle and a red ellipse. The suggested border of the partly preserved wing membrane after Jäger et al. (2018) is also marked (red transversal line). 9A. The whitish amorphous rock surface ventral to the cervical vertebral column. 9B. Specular enhancement image of 9A. Frequent occurrence of pycnofibres marked by a red triangle. The pycnofibre accumulation within the red circle might represent closely spaced neighbouring bifurcated Type 2 pycnofibres (pointed out by a red arrow). 9C. Interpretative drawing of 9B. 9D. Aktinofibril impressions close to the articulation of the first with the second phalanx of the right wing finger, especially well preserved within two orange-brown sediment surfaces. Also note the presence of aktinofibrils on the surface of the phalanges, visible in 9D as well as in 9E (recognisable by a grooved bony surface). 9E. Specular enhancement image of 9D. Aktinofibrils beyond the patagium border (and therefore laying on the bone surface of the phalanges) indicate their taphonomical displacement. 9F. Interpretative drawing of 9E demonstrating the spatial arrangement of the aktinofibril impressions. Not shown are the aktinofibrils on the bone surface.
FIGURE 2 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 2. Main slab (2A) and counter slab (2B) of the Scaphognathus crassirostris holotype, IGPB Goldfuss 1304a and b. Black rectangles and triangles illustrate the four different body regions in which soft part preservation is present: dorsal to the dorsal vertebral column until the base of the cervical vertebral column (1), ventral to the zeugopodial bones and next to the first and second phalanx of the fourth wing finger of the right wing (2), ventral to the cervical vertebral column (3), and the region enclosed by the zeugopodial and stylopodial bones of both wings (4). Images adapted from Jäger et al. (2018).
Spectral and trait data for Rapid estimates of leaf litter chemistry using reflectance spectroscopy
<p>Measuring the chemical traits of leaf litter is important for understanding plants' roles in nutrient cycles, including through nutrient resorption and litter decomposition, but conventional leaf trait measurements are often destructive and labor-intensive. Here, we develop and evaluate the performance of partial least-squares regression (PLSR) models that use reflectance spectra of intact or ground leaves to estimate leaf litter traits, including carbon and nitrogen concentration, carbon fractions, and leaf mass per area (LMA). Our analyses included more than 300 samples of senesced foliage from 11 species of temperate trees, including needleleaf and broadleaf species. Across all samples, we could predict each trait with moderate-to-high accuracy from both intact-leaf litter spectra (validation <em>R<sup>2</sup></em> = 0.543-0.941; %RMSE = 7.49-18.5) and ground-leaf litter spectra (validation <em>R<sup>2</sup></em> = 0.491-0.946; %RMSE = 7.00-19.5). Notably, intact-leaf spectra yielded better predictions of LMA. Our results support the feasibility of building models to estimate multiple chemical traits from leaf litter of a range of species. In particular, the success of intact-leaf spectral models allows non-destructive trait estimation in a matter of seconds, which could enable researchers to measure the same leaves over time in studies of nutrient resorption.</p>
An SI-traceable protocol for the validation of radiative transfer model-based reflectance simulation: datasets
<p>This data record contains datasets used in the study "An SI-traceable protocol for the validation of radiative transfer model-based reflectance simulation":</p> <ul> <li>The <code><span>final_design.ply</span></code> file contains the mesh corresponding to the final artefact design.</li> <li>The <code><span>material_measurements.nc</span></code> file contains goniophotometer records for the material reflectance.</li> <li>The <code><span>artefact_measurements.nc</span></code> file contains goniophotometer records for the artefact reflectance.</li> </ul>
HLWATER V1.0 Optical (water bodies Sentinel-2 TOA reflectance retrievals for 23/08/2019) - Western Nunavik (Subarctic Canada)
<p>This dataset refers to the retrieval of TOA reflectance from the Sentinel-2 L1C 10-m bands for 23/08/2019, having as reference the <a href="https://doi.org/10.5281/zenodo.12196313">Very High Resolution water body delineation dataset</a> computed with the <a href="https://doi.org/10.5281/zenodo.10203553">HLWATER V1.0 model</a> (<a href="https://doi.org/10.1016/j.rse.2024.114047">Freitas et al., 2024</a>) for Western Nunavik (Eastern Hudson Bay), Subarctic Canada. It covers a total area of 41,832 km2 within the latitudes 54° to 58° N and the longitudes 74° to 78° W.</p> <p>The dataset is composed of 167,755 water body reflectance retrievals. Additionally, 1 km2 hexagonal grids are provided with the calculation of the limnodiversity (diversity of water optical groups/colors). The optical groups were automatically defined using K-Means to 11 clusters, according to the highest Pseudo-F Score. Outputs are provided in shapefile and geodatabase formats.</p> <p>The manuscript detailing these outputs has been submitted to GIScience and Remote Sensing.</p>
Рис. 1. Вероятность обнаружения меченых животных (среΑнее ± ошибка) при пяти- и Αесятиметровых интерваΛах межΑу прикормочными станциями в Αвух экспериментах. По второму эксперименту расчеты сΑеΛаны ΑΛя резуΛьтатов отΛова в течение первых трех и поΛных Αесяти Αней. Значение «p» отражает уровень статистической значимости разΛичий межΑу ΑоΛями животных с меткой при Αвух интерваΛах Fig. 1. Probability of finding marked animals (average±standard error) between feeding stations placed at intervals of five and ten meters in the two experiments. In the second experiment, calculations were made for the results of trapping during the first three days and during the whole period of ten days. The p value reflects the statistical significance of differences between the fractions of animals with a mark for two types of intervals in Verification of the bottle-based method for estimating abundance of small mammals using biomarkers
Рис. 1. Вероятность обнаружения меченых животных (среΑнее ± ошибка) при пяти- и Αесятиметровых интерваΛах межΑу прикормочными станциями в Αвух экспериментах. По второму эксперименту расчеты сΑеΛаны ΑΛя резуΛьтатов отΛова в течение первых трех и поΛных Αесяти Αней. Значение «p» отражает уровень статистической значимости разΛичий межΑу ΑоΛями животных с меткой при Αвух интерваΛах Fig. 1. Probability of finding marked animals (average±standard error) between feeding stations placed at intervals of five and ten meters in the two experiments. In the second experiment, calculations were made for the results of trapping during the first three days and during the whole period of ten days. The p value reflects the statistical significance of differences between the fractions of animals with a mark for two types of intervals
Figure 1 in Growth regulators and their reflection on different hop genotypes cultivated under in vitro conditions
Figure 1. Explants of a hop genotype, grown in different culture media (yellow, blue and pink). Each medium provided different development behavior for the number of nodal segments. The larger the number of nodal segments, the more new plants will be obtained.
Figure 2 in Growth regulators and their reflection on different hop genotypes cultivated under in vitro conditions
Figure 2. Estimates of the direct and indirect effects of the variables root length (RL), shoot height (SH) and number of shoots (NS) on the variable number of nodal segments (NNS) (main variable).
Data for: Biogeography of oribatid mites (Acari) reflects their ancient origin and points to Southeast Asia as centre of radiation
<p>Understanding the worldwide distribution of species has fascinated scientists at least since Alfred Russel Wallace. Global patterns of belowground biodiversity may fundamentally differ from those of aboveground organisms. Here, we investigated the global distribution of oribatid mites in five biogeographic regions including North America, South America, Eurasia, Africa, and Oceania using a world list on the distribution of ~11,400 described species (including subspecies) at species, genera, and family levels. We found that most “endemic” (i.e., only occurring in one of the regions) species (4297) and also genera (143) occurred in Eurasia indicating that this region was the centre of radiation of oribatid mites. Within Eurasia, oribatid mite diversity was highest in Southeast Asia (1975 species) likely reflecting the long tropical history of this region (at least 200 million years), and also high fluctuations in water levels and island formation on the Sunda Shield. On a family level, oribatid mite diversity did not differ between biogeographic regions indicating that oribatid mites are much older than the tropics and older than the existence of Pangaea supporting the view of their origin in the early Palaeozoic. Finally, among the 55 species that occurred in all biogeographic regions nearly 50 % reproduce by thelytoky and colonize high latitude ecosystems, indicating that compared to sexual species a disproportionally high number of parthenogenetic species are distributed worldwide suggesting that they possess a general-purpose genotype. The other ~50 % sexuals predominantly occur in tropical/subtropical regions across biogeographic regions supporting the view that resource shortage in tropical regions favours sex. Our findings highlight the importance of biogeographical studies of soil animals to better understand their diversity, distribution, and life history strategies. </p>
Landsat-based Spectral Indices for pan-EU 2000-2022 - Bimonthly predictor (2022-05-01/2022-06-30): Reflectance bands
<h2><strong>Data Information</strong></h2> <p>This dataset includes seven reflectance bands: blue, green, red, nir, swir1, swir2, and thermal, for the period 2022-05-01/2022-06-30.</p> <h2><strong>As a Part of a Data Cube</strong></h2> <p>This data represents a subset of the <a href="../records/10776892">Time-series of Landsat-based Spectral Indices (EU, 30m) data cube</a>. For a comprehensive overview and full dataset information, please visit the landing page of this data cube using the provided link.</p> <ul> <li>To cite this dataset, refer to the DOI available on the landing page.</li> <li>To access other data layers in the data cube, use the navigation catalog on the landing page as well.</li> </ul> <h2><strong>Support</strong></h2> <p>If you discover a bug, artifact, or inconsistency, or if you have a question, please raise a <a href="https://github.com/AI4SoilHealth/SoilHealthDataCube/issues">Github Issue</a>!</p>
Landsat-based Spectral Indices for pan-EU 2000-2022 - Bimonthly predictor (2000-09-01/2000-10-31): Reflectance bands
<h2><strong>Data Information</strong></h2> <p>This dataset includes seven reflectance bands: blue, green, red, nir, swir1, swir2, and thermal, for the period 2000-09-01/2000-10-31.</p> <h2><strong>As a Part of a Data Cube</strong></h2> <p>This data represents a subset of the <a href="../records/10776892">Time-series of Landsat-based Spectral Indices (EU, 30m) data cube</a>. For a comprehensive overview and full dataset information, please visit the landing page of this data cube using the provided link.</p> <ul> <li>To cite this dataset, refer to the DOI available on the landing page.</li> <li>To access other data layers in the data cube, use the navigation catalog on the landing page as well.</li> </ul> <h2><strong>Support</strong></h2> <p>If you discover a bug, artifact, or inconsistency, or if you have a question, please raise a <a href="https://github.com/AI4SoilHealth/SoilHealthDataCube/issues">Github Issue</a>!</p>
Data set for "Columnar clusters in the human motion complex reflect consciously perceived motion axis"
<p>Accompanying data for manuscript “Columnar clusters in the human motion complex reflect consciously perceived motion axis” written by Marian Schneider, Valentin Kemper, Thomas Emmerling, Federico De Martino, Rainer Goebel, submitted, November 2018.</p> <p>Imaging files<br> -------------<br> * T1w and PDw images, only acquired in session 1<br> * 2 runs task-MotLoc, only acquired in session 2<br> * 5-6 runs task-ambiguous (called "Experiment 1" in accompanying manuscript, divided across 2 scanning sessions)<br> * 5-6 runs task-unambiguous (called "Experiment 2" in accompanying manuscript, divided across 2 scanning sessions)</p> <p><br> Acquisition details<br> -------------------<br> For visualization of the functional results, we acquired scans with structural information in the first scanning session. At high magnetic fields, MR images exhibit high signal intensity variations that result from heterogeneous RF coil profiles. We therefore acquired both T1w images and PDw images using a magnetization-prepared 3D rapid gradient-echo (3D MPRAGE) sequence (TR: 3100 ms (T1w) or 1440 ms (PDw), voxel size = 0.6 mm isotropic, FOV = 230 x 230 mm2, matrix = 384 x 384, slices = 256, TE = 2.52 ms, FA = 5°). Acquisition time was reduced by using 3× GRAPPA parallel imaging and 6/8 Partial Fourier in phase encoding direction (acquisition time (TA): 8 min 49 s (T1w) and 4 min 6 s (PDw)).</p> <p>To determine our region of interest, we acquired two hMT+ localiser runs. We used a 2D gradient echo (GE) echo planar imaging (EPI) sequence (1.6 mm isotropic nominal resolution; TE/TR = 18/2000 ms; in-plane field of view (FoV) 150×150 mm; matrix size 94 x 94; 28 slices; nominal flip angle (FA) = 69°; echo spacing = 0.71 ms; GRAPPA factor = 2, partial Fourier = 7/8; phase encoding direction head - foot; 240 volumes). We ensured that the area of acquisition had bilateral coverage of the posterior inferior temporal sulci, where we expected the hMT+ areas. Before acquisition of the first functional run, we collected 10 volumes for distortion correction - 5 volumes with the settings specified here and 5 more volumes with identical settings but opposite phase encoding (foot - head), here called "phase1" and "phase2".</p> <p>For the sub-millimetre measurements (Experiments 1: here called "task-ambiguous" and Experiments 2: here called "task-unambiguous"), we used a 2D GE EPI sequence (TE/TR = 25.6/2000 ms; in-plane FoV 148×148 mm; matrix size 186 x 186; slices = 28; nominal FA = 69°; echo spacing = 1.05 ms; GRAPPA factor = 3, partial Fourier = 6/8; phase encoding direction head - foot; 300 volumes), yielding a nominal resolution of 0.8 mm isotropic. Placement of the small functional slab was guided by online analysis of the hMT+ localizer data recorded immediately at the beginning of the first session. This allowed us to ensure bilateral coverage of area hMT+ for every subject. In the second scanning session, the slab was placed using Siemens auto-align functionality and manual corrections. Before acquisition of the first functional run, we collected 10 volumes for distortion correction (5 volumes with opposite phase encoding: foot - head). During acquisition, runs for the ambiguous and unambiguous motion experiments were interleaved.</p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.