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240 results for “Tissue imaging”
MALDI FTICR MS imaging data of pancreatic mouse tissue
<p>Preprocessed imaging mass spectrometry data (.imzML format) for mouse pancreatic Islets of Langerhans. Detailed information is given in the publication by Prade & Kunzke et al. "De novo discovery of metabolic heterogeneity with immunophenotype-guided imaging mass spectrometry" (currently in revision).</p>
Images supporting: Nondestructive, quantitative viability analysis of 3D tissue cultures using machine learning image segmentation
<p>Two image datasets (as zip files) including all images analyzed in the manuscript Nondestructive, quantitative viability analysis of 3D tissue cultures using machine learning image segmentation. Images are of pancreatic adenocarcinoma (PDAC) cystic spheroid samples grown in either BME or Matrigel. Some images have background noise in the form of iron oxide nanoparticles introduced to them.</p>
Accompanying dataset for: "IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues"
<p>Mouse datasets were acquired using the manual IBEX multiplex imaging protocol and accompany the manuscript “IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues”, A. Radtke <em>et al.</em>, 2020, PNAS.</p> <p>All image data are stored using the <a href="https://imaris.oxinst.com/support/imaris-file-format">Imaris file format</a>. To view these multi-channel images, you can either use one of these free viewers, <a href="https://imaris.oxinst.com/imaris-viewer">Imaris viewer</a>, <a href="https://imagej.net/Fiji">Fiji</a>.</p> <p>Each experiment has an associated imaging meta-data file in xlsx format and the resulting image in Imaris format.</p> <p><strong>Mouse spleen (Manual)</strong></p> <p>Dataset is a 16 parameter IBEX experiment performed on a mouse spleen section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse thymus (Manual)</strong></p> <p>Dataset is a 26 parameter IBEX experiment performed on a mouse thymus section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse lung (Manual)</strong></p> <p>Dataset is a 23 parameter IBEX experiment performed on a mouse lung section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.379 µm), y (0.379 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse small intestine (Manual)</strong></p> <p>Dataset is a 20 parameter IBEX experiment performed on a mouse small intestine section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse liver (Manual)</strong></p> <p>Dataset is an 18 parameter IBEX experiment performed on a liver section from a LysM-tdtomato reporter mouse labeled with antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse naive lymph node (Manual)</strong></p> <p>Dataset is a 41 parameter IBEX experiment performed on a mouse lymph node section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Mouse immunized lymph node (Manual)</strong></p> <p>Dataset is a 41 parameter IBEX experiment performed on a mouse lymph node section labeled with the nuclear marker JOJO-1 and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p>
Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue - IMC+RNAScope images
<p><span>Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides.<span> </span>We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.</span></p>
Data and code for publication: A simple preparation protocol for shipping and storage of tissue sections for laser ablation-inductively coupled plasma-mass spectrometry imaging
<p>Data & Code release for publication:</p> <p>Rebecca Buchholz, Sebastian Krossa, Maria K Andersen, Michael Holtkamp, Michael Sperling, Uwe Karst, May-Britt Tessem, A simple preparation protocol for shipping and storage of tissue sections for laser ablation-inductively coupled plasma-mass spectrometry imaging, <em>Metallomics</em>, Volume 14, Issue 3, March 2022, mfac013, <a href="https://doi.org/10.1093/mtomcs/mfac013">https://doi.org/10.1093/mtomcs/mfac013</a></p> <p>Python code for LA ICP MS imaging data segmentation</p> <p>Code & Data also on <a href="https://github.com/sekro/la-icp-msi_segmentation">github</a></p> <p>Thresholding based segmentation of LA-ICP-MS imaging data</p> <p>Description</p> <p><a href="https://github.com/sekro/la-icp-msi_segmentation/blob/master/src/main.py">src/main.py</a> - run this to process LA ICP MS data in data folder - generates matplotlib.figures - project specific setup <a href="https://github.com/sekro/la-icp-msi_segmentation/blob/master/src/laicpms_data_handler.py">src/laicpms_data_handler.py</a> - contains object to import, handle and segment (shimadzu) raw data</p> <p>Dependencies</p> <p>Python 3.8.1 or newer</p> <p>For packages see <a href="https://github.com/sekro/la-icp-msi_segmentation/blob/master/requirements.txt">requirements.txt</a></p> <p>Data</p> <p>LA-ICP-MS imaging data of human prostate tissue of the elements Zn, Fe & P. Details on data generation & collection in <a href="https://doi.org/10.1093/mtomcs/mfac013">publication</a>. LA-ICP-MS imaging data as plain text files (comma-separated values)</p> <ul> <li>Condition 1 = fresh frozen (FF)</li> <li>Condition 2 = room temperature vacuum dried and sealed (RTV)</li> <li>Condition 3 = formalin fixed (FFix)</li> <li>Condition 4 = formalin fixed, paraffin sealed (FFPS)</li> </ul> <p>3 replicate sectioning sets named A, B, C</p> <p>File-naming: LA_Data_CISN1.csv, where I = [1, 2, 3, 4] is indicating the condition used and N = [A, B, C] is indicating the replicate set</p> <p>License</p> <p>Data</p> <p>CC-BY 4.0 - respective <a href="https://github.com/sekro/la-icp-msi_segmentation/blob/master/data/LICENSE">LICENSE</a> file in data folder</p> <p>Source code</p> <p>MIT - respective <a href="https://github.com/sekro/la-icp-msi_segmentation/blob/master/src/LICENSE">LICENSE</a> file in src folder</p>
Text-fig. 2. SEM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in oblique lateral view showing remains of calyx and slightly semi-inferior ovary with elongated apical style (a); note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities and the stomata-like secretory structures on the upper portion of the ovary (arrows) that are interpreted as nectariferous (b). c: Detail of ovary surface showing secretory stomata-like structures (arrows). d: Flower in lateral view showing fragmentary calyx and broken slightly semi-inferior ovary with secretory stomata-like structures; note the point of attachment of the central placenta (pl). e: Cluster of seeds removed from the ovary in (d) showing reticulate surface. f: Outer (abaxial) surface of calyx lobe showing the slightly pointed papillae and scattered, fine trichomes (arrows). g: Triaperturate pollen grains from the ovary surface. Specimens, Mira 100-S153146 (a, b), Mira 100-S170155 (c), Mira 100-S101266 (d, e), Mira 105-S100732 (f), Mira 100-S170125 (g). Scale bars = 600 µm (a, b, d), 300 µm (f), 100 µm (c, e), 10 µm (g). in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 2. SEM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in oblique lateral view showing remains of calyx and slightly semi-inferior ovary with elongated apical style (a); note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities and the stomata-like secretory structures on the upper portion of the ovary (arrows) that are interpreted as nectariferous (b). c: Detail of ovary surface showing secretory stomata-like structures (arrows). d: Flower in lateral view showing fragmentary calyx and broken slightly semi-inferior ovary with secretory stomata-like structures; note the point of attachment of the central placenta (pl). e: Cluster of seeds removed from the ovary in (d) showing reticulate surface. f: Outer (abaxial) surface of calyx lobe showing the slightly pointed papillae and scattered, fine trichomes (arrows). g: Triaperturate pollen grains from the ovary surface. Specimens, Mira 100-S153146 (a, b), Mira 100-S170155 (c), Mira 100-S101266 (d, e), Mira 105-S100732 (f), Mira 100-S170125 (g). Scale bars = 600 µm (a, b, d), 300 µm (f), 100 µm (c, e), 10 µm (g).
Text-fig. 1. SEM images of flowers of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in lateral view showing elongated pedicel, narrowly triangular sepals and elongated protruding style (a); note the large openings in the floral tissue and pedicel (asterisks) interpreted as schizogenous secretory cavities. c: Flower in lateral view with portion of the calyx missing exposing the ovary wall and slightly raised nectariferous ring with probable stomata-like secretory structures (arrow). d: Flower in lateral view showing long pedicel and three of the five tepals; note the elongated narrowly triangular form of the sepals. e: Flower in oblique lateral view with portion of the calyx missing exposing the ovary and elongated style. f, g: Flowers in apical view showing the bases of five sepals (f) and apex of the five-parted ovary; note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities. Specimens, Mira 100-S170155 (a, holotype), Mira 100-S153145 (b, c, g), Mira 100- S101267 (d), Mira 105-S100732 (e), Mira 100-S101268 (f). Scale bars = 600 µm (a–g). in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 1. SEM images of flowers of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in lateral view showing elongated pedicel, narrowly triangular sepals and elongated protruding style (a); note the large openings in the floral tissue and pedicel (asterisks) interpreted as schizogenous secretory cavities. c: Flower in lateral view with portion of the calyx missing exposing the ovary wall and slightly raised nectariferous ring with probable stomata-like secretory structures (arrow). d: Flower in lateral view showing long pedicel and three of the five tepals; note the elongated narrowly triangular form of the sepals. e: Flower in oblique lateral view with portion of the calyx missing exposing the ovary and elongated style. f, g: Flowers in apical view showing the bases of five sepals (f) and apex of the five-parted ovary; note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities. Specimens, Mira 100-S170155 (a, holotype), Mira 100-S153145 (b, c, g), Mira 100- S101267 (d), Mira 105-S100732 (e), Mira 100-S101268 (f). Scale bars = 600 µm (a–g).
Text-fig. 5. Mastixiopsis nyssoides KIRCHH. a, b, g–n: Organic preservation. a, b: Lignitic, unpermineralized, early Eocene Dorset Pipe clays at Arne, V. 40762. a: Ventral view (original illustration from pl. 18, fig. 1 of Chandler 1962). b: Transverse fracture, somewhat distorted by compression. c–f: Pyrite permineralization. c: Ventral view, V. 22963(1) from Sheppey, originally listed as Mastixia cantiensis. d: Lateral view, V. 22969 from Sheppey (identified as Mastixia grandis by Reid and Chandler 1933: pl. 25, fig. 8). e: Equatorial transverse physical section from (c). f: Equatorial transverse physical section from (d). g: Detail of pericarp from (e), showing endocarp formed of dense fibrous tissue, surrounded by mesocarp of anticlinally oriented larger cells. h: Detail of pericarp from (f). i–n: Type material from Eocene of Riestadt, Germany, MNB. i: Ventral view. j, k: Ventral and apical views of holotype. l: View of the transversely fractured surface from (j) showing horseshoe shaped locule. m: Equatorial transverse physical cut of the specimen in (i); note yellow resin cavity (arrow). n: Scanning electron microscopy of pericarp from (l) with locule lining at lower edge of image. Note dense endocarp tissue composed of small cells (fibres and sclereids), extending about 3/5 of distance to periphery, surrounded by mesocarp of larger, anticlinally oriented cells. Scale bars 1 cm in (a–f), (i–k), 1 mm in (g), 2 mm in (h), 3 mm in (l), m, 250 Μm in (n). Bar in (d) applies also to (c). Bar in (l) also applies to (m). Bar in (i) also applies to (j) and (k). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 5. Mastixiopsis nyssoides KIRCHH. a, b, g–n: Organic preservation. a, b: Lignitic, unpermineralized, early Eocene Dorset Pipe clays at Arne, V. 40762. a: Ventral view (original illustration from pl. 18, fig. 1 of Chandler 1962). b: Transverse fracture, somewhat distorted by compression. c–f: Pyrite permineralization. c: Ventral view, V. 22963(1) from Sheppey, originally listed as Mastixia cantiensis. d: Lateral view, V. 22969 from Sheppey (identified as Mastixia grandis by Reid and Chandler 1933: pl. 25, fig. 8). e: Equatorial transverse physical section from (c). f: Equatorial transverse physical section from (d). g: Detail of pericarp from (e), showing endocarp formed of dense fibrous tissue, surrounded by mesocarp of anticlinally oriented larger cells. h: Detail of pericarp from (f). i–n: Type material from Eocene of Riestadt, Germany, MNB. i: Ventral view. j, k: Ventral and apical views of holotype. l: View of the transversely fractured surface from (j) showing horseshoe shaped locule. m: Equatorial transverse physical cut of the specimen in (i); note yellow resin cavity (arrow). n: Scanning electron microscopy of pericarp from (l) with locule lining at lower edge of image. Note dense endocarp tissue composed of small cells (fibres and sclereids), extending about 3/5 of distance to periphery, surrounded by mesocarp of larger, anticlinally oriented cells. Scale bars 1 cm in (a–f), (i–k), 1 mm in (g), 2 mm in (h), 3 mm in (l), m, 250 Μm in (n). Bar in (d) applies also to (c). Bar in (l) also applies to (m). Bar in (i) also applies to (j) and (k).
FIGURE 12 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 12. Distribution of the different soft tissue types occurring on the main slab of the Scaphognathus crassirostris holotype IGPB Goldfuss 1304a, illustrated in a modified version of Figure 2A. This Figure functions as a guide for the respective location of the soft part types intensively described in the manuscript and the captions to give an overview about their spatial distribution and their occurrence on the main slab, supported by the interpretative drawings of the soft tissues. Pycnofibre Type 2 (smaller red and yellow circles), Type 3 (orange circle), Type 4 (red rectangle), Type 5 (larger red circle), Type 6 (green circle), aktinofibrils (red ellipse), and putative patagium vessels marked by red transverse lines.
FIGURE 5 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 5. 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 5D). Scale bar for all illustrations equals 10 mm. 5A-5B. Caudal region dorsal to the dorsal vertebral column (lower right corner of both images) and next to the semi-circular indent, illustrated under different lighting conditions. 5C. Sketch of Figure 5A and 5B showing the appearance and the orientation of the pycnofibres under normal light. 5D-5E. Pycnofibres dorsal to the first anterior dorsal vertebrae (lower right corner), showing a striking pycnofibre accumulation under normal light (5D) as well as under the specular enhancement mode (5E). Note the spreading of pycnofibres in a radially symmetrical pattern from an arc-like starting point (red arrows, starting point marked by a red arc in 5E-5F). Also, note the branching in the dorsalmost part of the whitish limestone surface (orange circle in 5D-5F). 5F. Interpretative drawing of 5D and 5E, illustrating the arrangement of the pycnofibre impressions under normal light.
FIGURE 8 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 8. Close-up RTIViewer snapshots of the region ventral to the zeugopodial bones of the right wing on the counter slab, taken under different lighting conditions, but all processed using the specular enhancement mode (except for 8A). Scale bar for all illustrations equals 10 mm, except for 8E (1 mm). Markings for various pycnofibre types used throughout this Figure: the location of aktinofibrils impressions is marked by a red rectangle, the direction in which pycnofibre impressions point is highlighted by red arrows, the Type 2 pycnofibre is illustrated by a red circle. 8A. The whitish amorphous rock surface with pycnofibres between the zeugopodial bones of the right wing (upper right corner) and the first two phalanges of the right wing finger (lower left corner). Note first type pycnofibre impressions (red lines). The locality of overlapping impressions is marked by an orange circle in 8A and 8B (although not well visible in the image). 8B. Idealised sketch of Figure 8A after comparing several RTI images with each other to better visualise the trend of the decreasing abundance of crossing/ overlapping pycnofibres. Note that a trend of opposing impression directions seems to exist in this area of the counter slab (see the two red arrows). 8C. Specular enhancement image depicting the lower image part of 8A encompassing a wider field of vision. Aktinofibrils-like impressions heading for the lower right edge of the image (red arrows within the orange rectangle). 8D. Sketch of 8C. 8E. Enlarged close-up of the Type 2 pycnofibre. A much smaller terminal bifurcation is indicated (red arrow), suggesting that it might even be another type of bifurcated pycnofibre. 8F. Sketch of 8E, illustrating the smaller terminal bifurcation (yellow circle). 8G, 8I. The inconsistent appearance of the pycnofibres directly ventral to the articulation of the metacarpal bones with the phalanges of the right wing finger, taking on interesting shapes depending on the direction of incident light (red oval in 8G and also indicated in 8H). At some places, the pycnofibre impressions cross each other at specific angles (marked by two red angles in 8G and 8I). 8H. Sketch of 8G to highlight the oval shape of an accumulation of impressions.
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.
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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.