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Supplemental Data from the article "The SmARTR pipeline: a modular workflow for the cinematic rendering of 3D scientific imaging data"
<h1><strong>Please, refer to <a href="https://github.com/MeVisLab/SmARTR-Networks">this GitHub repository</a> for additional info, updates, issue reports, and discussion<br></strong></h1> <p><strong>A collection of configuration files (SmARTR networks) published in "<a href="https://doi.org/10.1016/j.isci.2024.111475">The SmARTR Pipeline: a modular workflow for the cinematic rendering of 3D scientific imaging data</a>", enabling the creation of cinematic (photorealistic) renderings of 3D data in the FREE software <a href="https://www.mevislab.de/download">MeVisLab</a><br></strong></p> <ul> <li>Each folder in the archive contains one or more SmARTR network files, the scan and mask files required for the practical examples detailed in the <a href="https://www.cell.com/cms/10.1016/j.isci.2024.111475/attachment/8d79036b-acb6-4cda-a5ff-f56317691ebc/mmc1.pdf">Supplemental Data</a> of the article, and an additional folder with LUT presets.</li> </ul>
Piprahwa (Siddharthnagar district, Uttar Pradesh). Rendering of reliquary inscription, from museum image.
<p>Piprahwa (Siddharthnagar district, Uttar Pradesh). Rendering of reliquary inscription, from museum image.</p>
Text-fig. 3. SRXTM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Volume renderings of flower bud in two different lateral views showing long pedicel, distinct calyx (ca) with almost equiaxial epidermal cells and corolla (co) with nearly smooth surface. c–e: Transverse sections (c, orthoslice xy1500; d, orthoslice xy1760; e, orthoslice xy1850) through flower bud at levels below the anthers showing stamen filaments (yellow) opposite the corolla lobes (co) and smaller staminodes (orange) in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 3. SRXTM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Volume renderings of flower bud in two different lateral views showing long pedicel, distinct calyx (ca) with almost equiaxial epidermal cells and corolla (co) with nearly smooth surface. c–e: Transverse sections (c, orthoslice xy1500; d, orthoslice xy1760; e, orthoslice xy1850) through flower bud at levels below the anthers showing stamen filaments (yellow) opposite the corolla lobes (co) and smaller staminodes (orange)
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings.
Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f).
Text-fig. 49. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–e) images of "Foveolate seed sp. 1"; Catefica locality, Portugal. a) Lateral view of seed showing foveolate surface; note the slightly pointed hilar-micropylar region with the preservation of a presumed secretion (arrow) from the micropyle; b) Detail of seed surface showing shallow pitting and very faint outlines of the undulate anticlinal walls of the exotestal cells; c) Longitudinal section (volume rendering cut between orthoslices yz0450 and yz0460) through the middle of the seed showing the slightly pointed hilarmicropylar region and the rounded chalazal region; note the thick exotesta of the outer integument composed of thick-walled palisade-like cells (oi); note partial preservation of large cells of the nutritive tissue (nu) and the smaller cells of the embryo (em) at the micropylar end of the seed; d, e) Longitudinal sections (d, orthoslice xz0750, e, orthoslice yz0485) through middle of the seed perpendicular to each other showing the hilar-micropylar region with the preservation of a presumed secretion from micropyle (e, arrow), thick palisade-like cells of outer integument (oi), larger cells of the nutritive tissue (nu) and remains of the smaller cells of the embryo (em). Specimen, Catefica 49-S172316 (a–e). Scale bars = 300 Μm (a, c–e), 50 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 49. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–e) images of "Foveolate seed sp. 1"; Catefica locality, Portugal. a) Lateral view of seed showing foveolate surface; note the slightly pointed hilar-micropylar region with the preservation of a presumed secretion (arrow) from the micropyle; b) Detail of seed surface showing shallow pitting and very faint outlines of the undulate anticlinal walls of the exotestal cells; c) Longitudinal section (volume rendering cut between orthoslices yz0450 and yz0460) through the middle of the seed showing the slightly pointed hilarmicropylar region and the rounded chalazal region; note the thick exotesta of the outer integument composed of thick-walled palisade-like cells (oi); note partial preservation of large cells of the nutritive tissue (nu) and the smaller cells of the embryo (em) at the micropylar end of the seed; d, e) Longitudinal sections (d, orthoslice xz0750, e, orthoslice yz0485) through middle of the seed perpendicular to each other showing the hilar-micropylar region with the preservation of a presumed secretion from micropyle (e, arrow), thick palisade-like cells of outer integument (oi), larger cells of the nutritive tissue (nu) and remains of the smaller cells of the embryo (em). Specimen, Catefica 49-S172316 (a–e). Scale bars = 300 Μm (a, c–e), 50 Μm (b).
Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e).
Text-fig. 42. Scanning electron microscope (SEM, a, b, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d, f–g) images of "Tricarpellate flower sp. 1"; Catefica locality, Portugal. a, b) Flower bud in two different lateral views showing semiinferior ovary and perianth; c) Longitudinal section (orthoslice yz0340) through flower bud in (a and b) showing the semi-inferior gynoecium and perigynous insertion of other floral parts; d) Volume rendering of flower bud with pedicel preserved; note the depression/split in one of the corner apparently separating two perianth lobes of the outer perianth whorl (t-o) and exposing one tepal of the inner whorl (t-i); e) Flower bud with pedicel preserved; note broad tepals of the outer whorl (t-o) and tepal of the inner whorl abraded exposing a broad stamen (st); f, g) Transverse sections through flower bud in (a and b) at two different levels above the insertion of the perianth (f, rec-file 1310; g, xy0280) showing the trimerous organization of the flower and the free, laterally flattened carpels; yellow indicates the two whorls of the androecium, each with three stamens. Specimens, Catefica 50-S171520 (a–c, f), Catefica 50-S174902 (d), Catefica MM154-P0271 (e), Catefica 49-S175354 (g). Scale bars = 300 Μm (a–e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 42. Scanning electron microscope (SEM, a, b, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d, f–g) images of "Tricarpellate flower sp. 1"; Catefica locality, Portugal. a, b) Flower bud in two different lateral views showing semiinferior ovary and perianth; c) Longitudinal section (orthoslice yz0340) through flower bud in (a and b) showing the semi-inferior gynoecium and perigynous insertion of other floral parts; d) Volume rendering of flower bud with pedicel preserved; note the depression/split in one of the corner apparently separating two perianth lobes of the outer perianth whorl (t-o) and exposing one tepal of the inner whorl (t-i); e) Flower bud with pedicel preserved; note broad tepals of the outer whorl (t-o) and tepal of the inner whorl abraded exposing a broad stamen (st); f, g) Transverse sections through flower bud in (a and b) at two different levels above the insertion of the perianth (f, rec-file 1310; g, xy0280) showing the trimerous organization of the flower and the free, laterally flattened carpels; yellow indicates the two whorls of the androecium, each with three stamens. Specimens, Catefica 50-S171520 (a–c, f), Catefica 50-S174902 (d), Catefica MM154-P0271 (e), Catefica 49-S175354 (g). Scale bars = 300 Μm (a–e).
Text-fig. 6. Scanning electron microscope (SEM, a, g, h) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b–f) images of fruits and pollen grains of Canrightiopsis crassitesta (a–c, g, h) and fruit of Canrightiopsis intermedia (d–f); Catefica locality, Portugal. a) Dorsal view of fruit showing rim of hypanthium (arrowheads); b) Surface rendering of longitudinal section in the median plane of fruit (cut between orthoslices yz0440-0510) showing the thin fruit wall, thick endotesta of the seed coat (en, dark blue) and the orthotropous, pendent seed with the chalaza (ch) near the fruit apex and the micropyle (mi) at the fruit base; note the tiny embryo (emb) adjacent to the micropyle at the base of the fruit; c) Longitudinal section (orthoslice xz0511) through the seed wall showing the thick, finely crystalliferous endotesta (en) surrounding the nutritive tissue of the seed; d) Surface rendering of fruit in dorsal view showing rim of the hypanthium (arrowheads) and apical stigmatic region (st); e) Surface rendering of longitudinal section of fruit in (d) (cut at orthoslice xz0560) showing the crystalliferous endotesta (en, dark blue) and the inner tissues of the seed; f) Longitudinal section (orthoslice xz0560) through fruit and seed showing the finely crystalliferous endotesta (en) and thin fruit wall (fr); g, h) Pollen grains from apical region of fruit showing poorly defined margin of the single colpus, reticulate tectum and muri ornamented by minute verrucae. Specimens, Catefica 343-S174311 (a), Catefica 49-S174159 (b, c), Catefica 50-S174905 (d–f), Catefica 342-S122089 (g, h). Scale bars = 300 Μm (a, b, d, e), 150 Μm (c, f), 6 Μm (g), 3 Μm (h). g, h published with permission from Grana. in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 6. Scanning electron microscope (SEM, a, g, h) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b–f) images of fruits and pollen grains of Canrightiopsis crassitesta (a–c, g, h) and fruit of Canrightiopsis intermedia (d–f); Catefica locality, Portugal. a) Dorsal view of fruit showing rim of hypanthium (arrowheads); b) Surface rendering of longitudinal section in the median plane of fruit (cut between orthoslices yz0440-0510) showing the thin fruit wall, thick endotesta of the seed coat (en, dark blue) and the orthotropous, pendent seed with the chalaza (ch) near the fruit apex and the micropyle (mi) at the fruit base; note the tiny embryo (emb) adjacent to the micropyle at the base of the fruit; c) Longitudinal section (orthoslice xz0511) through the seed wall showing the thick, finely crystalliferous endotesta (en) surrounding the nutritive tissue of the seed; d) Surface rendering of fruit in dorsal view showing rim of the hypanthium (arrowheads) and apical stigmatic region (st); e) Surface rendering of longitudinal section of fruit in (d) (cut at orthoslice xz0560) showing the crystalliferous endotesta (en, dark blue) and the inner tissues of the seed; f) Longitudinal section (orthoslice xz0560) through fruit and seed showing the finely crystalliferous endotesta (en) and thin fruit wall (fr); g, h) Pollen grains from apical region of fruit showing poorly defined margin of the single colpus, reticulate tectum and muri ornamented by minute verrucae. Specimens, Catefica 343-S174311 (a), Catefica 49-S174159 (b, c), Catefica 50-S174905 (d–f), Catefica 342-S122089 (g, h). Scale bars = 300 Μm (a, b, d, e), 150 Μm (c, f), 6 Μm (g), 3 Μm (h). g, h published with permission from Grana.
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d).
Text-fig. 33. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a, c) and scanning electron microscope (SEM, b, d) images of Paisia pantoporata (a–c) and?Paisia sp. (d); Catefica locality, Portugal. a) Lateral view (volume rendering) of flower showing the carpels (c) and the fleshy tepals (t) that have a slightly bulge near the base; b) Pollen grains in situ from stamen showing scattered pores and spiny supratectal ornamentation; c) Transverse section (orthoslice xz1024) through flower showing the pentamerous organization with five tepals (green) five stamens (yellow) and five carpels (red) all on the same radii; d) Lateral view of floral structure with three free carpels borne on the swollen receptacle that has poorly defined facets at the apex indicating the former presence of perianth parts. Specimens, Catefica 49-S101214 (a, c), Catefica 50-S170188 (b), Catefica MM125-P0292 (d). Scale bars = 300 Μm (a, c, d), 6 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 33. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a, c) and scanning electron microscope (SEM, b, d) images of Paisia pantoporata (a–c) and?Paisia sp. (d); Catefica locality, Portugal. a) Lateral view (volume rendering) of flower showing the carpels (c) and the fleshy tepals (t) that have a slightly bulge near the base; b) Pollen grains in situ from stamen showing scattered pores and spiny supratectal ornamentation; c) Transverse section (orthoslice xz1024) through flower showing the pentamerous organization with five tepals (green) five stamens (yellow) and five carpels (red) all on the same radii; d) Lateral view of floral structure with three free carpels borne on the swollen receptacle that has poorly defined facets at the apex indicating the former presence of perianth parts. Specimens, Catefica 49-S101214 (a, c), Catefica 50-S170188 (b), Catefica MM125-P0292 (d). Scale bars = 300 Μm (a, c, d), 6 Μm (b).
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d).
Text-fig. 20. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a) and scanning electron microscope (SEM, b–h) images of fruits of Appomattoxia sp. (a–d) and anther and pollen of Goczania rugosa (e–h); Catefica locality, Portugal. a) Surface rendering of fruit in lateral view showing densely spaced hairs, some with delicate coiled tips; b) Fruit in lateral view showing short, densely spaced hairs and apical stigmatic region; c, d) Detail of fruit surface and hairs from fruit in (b); e) Fragmentary anther showing four pollen sacs; f) Proximal view of pollen grains from an abraded anther showing microechinate surface of pollen wall and clusters of small, spiny orbicules; g, h) Proximal (g) and distal (h) views of pollen grains from an isolated pollen sac, showing short colpus (h), tectate pollen wall and microechinate surface ornamentation. Specimens, Catefica 49-S174913 (a), Catefica 49-S107794 (b–d), Catefica 50-S170391 (e), Catefica 49-S170138 (f), Catefica 49-S170143 (g, h). Scale bars = 300 Μm (a, b, e), 100 Μm (c), 50 Μm (d), 6 Μm (f–h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 20. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a) and scanning electron microscope (SEM, b–h) images of fruits of Appomattoxia sp. (a–d) and anther and pollen of Goczania rugosa (e–h); Catefica locality, Portugal. a) Surface rendering of fruit in lateral view showing densely spaced hairs, some with delicate coiled tips; b) Fruit in lateral view showing short, densely spaced hairs and apical stigmatic region; c, d) Detail of fruit surface and hairs from fruit in (b); e) Fragmentary anther showing four pollen sacs; f) Proximal view of pollen grains from an abraded anther showing microechinate surface of pollen wall and clusters of small, spiny orbicules; g, h) Proximal (g) and distal (h) views of pollen grains from an isolated pollen sac, showing short colpus (h), tectate pollen wall and microechinate surface ornamentation. Specimens, Catefica 49-S174913 (a), Catefica 49-S107794 (b–d), Catefica 50-S170391 (e), Catefica 49-S170138 (f), Catefica 49-S170143 (g, h). Scale bars = 300 Μm (a, b, e), 100 Μm (c), 50 Μm (d), 6 Μm (f–h).
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b).
Computer-rendered HDR and LDR 4k images database
<p>Realistic image computation mimics the natural process of acquiring pictures by simulating the physical interactions of light between all the objects, lights and cameras lying within a modelled 3D scene. This process is known as global illumination and was formalised by Kajiya with the following rendering Equation:<br> <span class="math-tex">\(\begin{equation} \label{eq:rendering_equation} L_o(x, \omega_o) = {L_e(x, \omega_o)} + \int_{\Omega}^{} {L_i(x, \omega_i)} \cdot f_r(x, \omega_i \rightarrow \omega_o) \cdot \cos \theta_i d\omega_i \end{equation}\)</span></p> <p>where:</p> <ul> <li> <span class="math-tex">\(L_o(x, \omega_o)\)</span> is the luminance traveling from point <span class="math-tex">\(x\)</span> in direction <span class="math-tex">\(\omega_o\)</span>;</li> <li><span class="math-tex">\(L_e(x, \omega_o)\)</span> is point <span class="math-tex">\(x\)</span> emitted luminance (it is null if point x does not lie on a ligth source surface);</li> <li>the integral represents the set of luminances <span class="math-tex">\(L_i\)</span>incident in <span class="math-tex">\(x \)</span> from the hemisphere of the directions <span class="math-tex">\(\Omega\)</span> and reflected in the direction <span class="math-tex">\(\omega_o\)</span>. The reflected luminances are weighted by the materials reflecting properties (bidirectionnal reflectance function <span class="math-tex">\(f_r(x, \omega_i \rightarrow \omega_o)\)</span>) and the cosinus of the incident angle.</li> </ul> <p>This equation cannot be analytically solved and Monte Carlo approaches are generally used to estimate the value of the pixels of the final image.</p> <p>This proposed dataset is composed of 32 points of view of photo realistics images with different level of samples (following the Monte Carlo approach) for each. Each image is 3840 × 2160 pixels in size. The most noisy image is of 2⁰ samples and the reference one (the most converged image obtained) is of 2²⁰ samples. The <a href="https://www.pbrt.org/index.html">pbrt</a> rendering engine (version 4) was used to generate these images.</p>
SD4EO - Physically Based Rendering images of crop fields (Sentinel-2 B2B3B4B8B11 & Sentinel-1 SAR)
<p>This dataset contains part of the results of the SD4EO project, including images corresponding to the use case of crop fields identification. The dataset contains images that have been simulated corresponding to different sensors of the Sentinel 1 and Sentinel 2 satellites and regarding 9 different types of crops. Each image in the dataset includes pixel-level labels for each element present in the image, ensuring perfect accuracy due to the synthetic nature of the images. This eliminates common errors in manual or semi-automatic labeling processes.</p> <p><strong>Multispectral images included</strong></p> <p>Sentinel 1: SAR (Synthetic Aperture Radar) images.<br>Sentinel 2: Images from bands 2, 3, 4, 8, and 11.</p> <p><strong>Image labeling</strong></p> <div> <table> <tbody> <tr> <td> <p><strong>Crop</strong></p> </td> <td> <p><strong>R</strong></p> </td> <td> <p><strong>G</strong></p> </td> <td> <p><strong>B</strong></p> </td> </tr> <tr> <td> <p>Alfalfa or lucerne</p> </td> <td> <p>47</p> </td> <td> <p>255</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>Barley</p> </td> <td> <p>35</p> </td> <td> <p>192</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>Fallow and bare soil</p> </td> <td> <p>25</p> </td> <td> <p>135</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>Oats</p> </td> <td> <p>118</p> </td> <td> <p>178</p> </td> <td> <p>105</p> </td> </tr> <tr> <td> <p>Other grain leguminous</p> </td> <td> <p>38</p> </td> <td> <p>79</p> </td> <td> <p>29</p> </td> </tr> <tr> <td> <p>Peas</p> </td> <td> <p>44</p> </td> <td> <p>217</p> </td> <td> <p>70</p> </td> </tr> <tr> <td> <p>Sunflower</p> </td> <td> <p>78</p> </td> <td> <p>123</p> </td> <td> <p>68</p> </td> </tr> <tr> <td> <p>Vetch</p> </td> <td> <p>33</p> </td> <td> <p>58</p> </td> <td> <p>28</p> </td> </tr> <tr> <td> <p>Wheat</p> </td> <td> <p>130</p> </td> <td> <p>255</p> </td> <td> <p>102</p> </td> </tr> </tbody> </table> </div> <p><br><strong>Image name convention</strong></p> <p>The name convention follows the next schema of fields, separated by the character “_”</p> <p>- ID number</p> <p>- Meters per pixel resolution</p> <p>- Month</p> <p>- Type of image (Sentinel 2 band, Sentinel 1 SAR or labels): B2B3B4, B8, B11, SAR, labels</p> <p><strong>Image formats</strong></p> <p>TIFF format is used to save each band with floating point precision in the original range of the satellite images.</p> <p>PNG format is used to display each band in normalized values [0..1].</p> <table> <tbody> <tr> <td> <p><strong>Type of data</strong></p> </td> <td> <p><strong>PNG range</strong></p> </td> <td> <p><strong>TIFF range</strong></p> </td> </tr> <tr> <td> <p>B2</p> </td> <td> <p>0 - 255</p> </td> <td> <p>0 - 2000</p> </td> </tr> <tr> <td> <p>B3</p> </td> <td> <p>0 - 255</p> </td> <td> <p>0 - 2500</p> </td> </tr> <tr> <td> <p>B4</p> </td> <td> <p>0 - 255</p> </td> <td> <p>0 - 3000</p> </td> </tr> <tr> <td> <p>B8</p> </td> <td> <p>0 - 255</p> </td> <td> <p>1180 - 5736</p> </td> </tr> <tr> <td> <p>B11</p> </td> <td> <p>0 - 255</p> </td> <td> <p>859 - 5648</p> </td> </tr> <tr> <td> <p>SAR</p> </td> <td> <p>0 - 255</p> </td> <td> <p>-31.45273 - -14.23931</p> </td> </tr> </tbody> </table> <p><strong>Creation and funding</strong></p> <p>All the images have been generated using a tool developed in Unity. This tool will be soon available to enable the generation of new datasets.</p> <p>This research work has been funded by the European Space Agency (ESA) under the FutureEO program and the SD4EO project (Contract No.: 4000142334/23/I-DT), supervised by the ESA Φ-lab.</p> <p><strong>License and attribution</strong></p> <p>This dataset is licensed under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> (CC BY 4.0).</p> <p>When using the images from this dataset, please attribute them as follows: "Synthetic images created by the research group ARTEC - IRTIC - University of Valencia".</p>
SD4EO - Physically Based Rendering images of human settlements for solar panel detection
<p>This dataset contains part of the results of the SD4EO project, including images corresponding to the use case of solar panel detection on human settlements. The dataset contains images that have been simulated corresponding to low altitude aerial images. Each image in the dataset includes pixel-level labels for each element present in the image, ensuring perfect accuracy due to the synthetic nature of the images. This eliminates common errors in manual or semi-automatic labeling processes.</p> <p><strong>Image labeling</strong></p> <p><strong>(Open Street Map color code)</strong></p> <div> <table> <tbody> <tr> <td> <p><strong>Element</strong></p> </td> <td> <p><strong>R</strong></p> </td> <td> <p><strong>G</strong></p> </td> <td> <p><strong>B</strong></p> </td> </tr> <tr> <td> <p>Road</p> </td> <td> <p>255</p> </td> <td> <p>255</p> </td> <td> <p>255</p> </td> </tr> <tr> <td> <p>Building</p> </td> <td> <p>196</p> </td> <td> <p>182</p> </td> <td> <p>171</p> </td> </tr> <tr> <td> <p>Highway</p> </td> <td> <p>232</p> </td> <td> <p>146</p> </td> <td> <p>162</p> </td> </tr> <tr> <td> <p>Industrial zone</p> </td> <td> <p>234</p> </td> <td> <p>203</p> </td> <td> <p>228</p> </td> </tr> <tr> <td> <p>Parking</p> </td> <td> <p>238</p> </td> <td> <p>238</p> </td> <td> <p>238</p> </td> </tr> <tr> <td> <p>Railway</p> </td> <td> <p>112</p> </td> <td> <p>112</p> </td> <td> <p>112</p> </td> </tr> <tr> <td> <p>Residential zone</p> </td> <td> <p>224</p> </td> <td> <p>223</p> </td> <td> <p>223</p> </td> </tr> <tr> <td> <p>Vegetation</p> </td> <td> <p>174</p> </td> <td> <p>223</p> </td> <td> <p>163</p> </td> </tr> <tr> <td> <p>Water</p> </td> <td> <p>170</p> </td> <td> <p>211</p> </td> <td> <p>223</p> </td> </tr> </tbody> </table> </div> <p>For solar panels masks white color is used to mark the pixels corresponding to solar panels.</p> <p><br><strong>Image name convention</strong></p> <p>The name convention follows the next schema of fields, separated by the character “_”</p> <p>- ID number</p> <p>- Sub ID number</p> <p>- Meters per pixel resolution</p> <p>- Type of image: color, labels, solarpanels</p> <p><strong>Creation and funding</strong></p> <p>All the images have been generated using a tool developed in Unity. This tool will be soon available to enable the generation of new datasets.</p> <p>This research work has been funded by the European Space Agency (ESA) under the FutureEO program and the SD4EO project (Contract No.: 4000142334/23/I-DT), supervised by the ESA Φ-lab.</p> <p><strong>License and attribution</strong></p> <p>This dataset <span>is</span> licensed under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> (CC <span>BY</span> <span>4.0</span>).</p> <p><span>When using the images from this dataset, please attribute them as follows: "Synthetic images created by the research group ARTEC - IRTIC - University of Valencia".</span></p>
Result of Show View Updates to Oversize image rendering
<p>Result of Show View Updates to Oversize image rendering</p>
Result of Show View Updates to Correct Size Image Rendering
<p>Result of Show View Updates to Correct Size Image Rendering </p>
Text-fig. 6. SRXTM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a: Volume rendering of flower in apical view showing five narrow calyx lobes; note that the apical part of the five-angled style is sealed (arrow). b: Volume rendering of flower (cut at orthoslice xy0796) showing transverse sections of calyx lobes with three distinct bundles indicated by arrows in one of the lobes, ovary wall (ow) and central placenta (pl) bearing numerous ovules (ov). c, d: Transverse sections of style (c, orthoslice xy0153; d, orthoslice xy0222) showing five angled form, sealed near apex (c) and with prominent central canal further farther down (d). e: Volume rendering of flower (cut at orthoslice xz1024) in longitudinal section showing calyx, semi-inferior ovary with ovary wall (ow), and central placenta (pl) bearing numerous ovules (ov). Specimen, Mira 100-S153145 (a–d). Scale bars = 600 µm (a, b, e), 100 µm (c, d). in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 6. SRXTM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a: Volume rendering of flower in apical view showing five narrow calyx lobes; note that the apical part of the five-angled style is sealed (arrow). b: Volume rendering of flower (cut at orthoslice xy0796) showing transverse sections of calyx lobes with three distinct bundles indicated by arrows in one of the lobes, ovary wall (ow) and central placenta (pl) bearing numerous ovules (ov). c, d: Transverse sections of style (c, orthoslice xy0153; d, orthoslice xy0222) showing five angled form, sealed near apex (c) and with prominent central canal further farther down (d). e: Volume rendering of flower (cut at orthoslice xz1024) in longitudinal section showing calyx, semi-inferior ovary with ovary wall (ow), and central placenta (pl) bearing numerous ovules (ov). Specimen, Mira 100-S153145 (a–d). Scale bars = 600 µm (a, b, e), 100 µm (c, d).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.