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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. 2. Scanning electron microscope (SEM, a, c–f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b, g) images of the flower of Mugideiriflora portugallica (a, b) and fruits, seeds and pollen of Canrightia resinifera (c–g); Catefica locality, Portugal. a) Oblique, apical view of flower showing multiparted organization with numerous laminar tepals, stamens that are rhomboidal and flattened in transverse section and carpels that are borne on the short conical apex of the receptacle; b) Transverse section (orthoslice xy0800) through basal part of flower showing the elongate bases of the laminar tepals and the flattened rhomboidal bases of the stamens; c) Fruit in lateral view showing irregular surface resulting from the abundant resin bodies in the fruit and hypanthium wall, scars from stamens on the rim of the hypanthium (arrowheads) and the lobed apical stigmatic region (st); d) Broken fruit with one or two seeds missing but showing three pendant, orthotropous seeds with pointed micropylar regions (mi) and a finely pitted crystalliferous endotesta; note the remains of the apical vascular bundles (vb); e) Single seed isolated from a fruit showing two distinct bundles (vb) still attached apically to the chalazal region of the seed, the pointed micropyle (mi) and the finely pitted surface of the crystalliferous endotesta; f) Monocolpate pollen from stigmatic region of fruit showing the long colpus and coarse reticulum; g) Transverse section (orthoslice xy0705) through a fruit showing four seeds all with radially elongated endothelium cells formed from the inner epidermis of the tegmen (asterisks). Specimens, Catefica 150-S174254 (a, b), Catefica 49-S170377 (c), Catefica 49-S170372 (d), Catefica 50-S170401 (e), Catefica 50-S170404 (f), Catefica 50-S174906 (g). Scale bars = 300 Μm (a–e, g), 6 Μm (f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 2. Scanning electron microscope (SEM, a, c–f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b, g) images of the flower of Mugideiriflora portugallica (a, b) and fruits, seeds and pollen of Canrightia resinifera (c–g); Catefica locality, Portugal. a) Oblique, apical view of flower showing multiparted organization with numerous laminar tepals, stamens that are rhomboidal and flattened in transverse section and carpels that are borne on the short conical apex of the receptacle; b) Transverse section (orthoslice xy0800) through basal part of flower showing the elongate bases of the laminar tepals and the flattened rhomboidal bases of the stamens; c) Fruit in lateral view showing irregular surface resulting from the abundant resin bodies in the fruit and hypanthium wall, scars from stamens on the rim of the hypanthium (arrowheads) and the lobed apical stigmatic region (st); d) Broken fruit with one or two seeds missing but showing three pendant, orthotropous seeds with pointed micropylar regions (mi) and a finely pitted crystalliferous endotesta; note the remains of the apical vascular bundles (vb); e) Single seed isolated from a fruit showing two distinct bundles (vb) still attached apically to the chalazal region of the seed, the pointed micropyle (mi) and the finely pitted surface of the crystalliferous endotesta; f) Monocolpate pollen from stigmatic region of fruit showing the long colpus and coarse reticulum; g) Transverse section (orthoslice xy0705) through a fruit showing four seeds all with radially elongated endothelium cells formed from the inner epidermis of the tegmen (asterisks). Specimens, Catefica 150-S174254 (a, b), Catefica 49-S170377 (c), Catefica 49-S170372 (d), Catefica 50-S170401 (e), Catefica 50-S170404 (f), Catefica 50-S174906 (g). Scale bars = 300 Μm (a–e, g), 6 Μm (f).

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).

opencc-by-4.0Apr 2023View details →

RESI Localization Microscopy Datasets

Localization Microscopy Datasets from this publication: https://doi.org/10.1038/s41586-023-05925-9. Archive contains all relevant .hdf5 datasets alongside information about file content.

Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (wtChR2-mEos3.2)

This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555) Zip file contains PALM measurements of HEK293 cells expressing ChR2WT fused with mEos3.2. Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames. Detailed protocols for sample preparation and data acquisition are described in the article. Some details are listed below. SAMPLE PREPARATION cell line: Flp-In™ T-REx™ 293 transfection method: modified calcium-phosphate transient transfection [1] fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature imaging buffer: PBS PALM ACQUISITION A custom-built setup for single-molecule localization microscopy is described in [2]. mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample). PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera: exposure time = 100 ms frame size = 512x512 pixels pixel size = 80 nm   [1] Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52. [2] Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073

Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (ChR2(C34A/C36A)-mEos3.2)

This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555) Zip file contains PALM measurements of HEK293 cells expressing ChR2C34A/C36A fused with mEos3.2. Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames. Detailed protocols for sample preparation and data acquisition are described in the article. Some details are listed below. SAMPLE PREPARATION cell line: Flp-In™ T-REx™ 293 transfection method: modified calcium-phosphate transient transfection [1] fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature imaging buffer: PBS PALM ACQUISITION A custom-built setup for single-molecule localization microscopy is described in [2]. mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample). PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera: exposure time = 100 ms frame size = 512x512 pixels pixel size = 80 nm   [1] Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52. [2] Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073

Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (b1AR-mEos3.2)

This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555) Zip file contains PALM measurements of HEK293 cells expressing ß1AR fused with mEos3.2. Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames. Detailed protocols for sample preparation and data acquisition are described in the article. Some details are listed below. SAMPLE PREPARATION cell line: Flp-In™ T-REx™ 293 transfection method: modified calcium-phosphate transient transfection [1] fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature imaging buffer: PBS PALM ACQUISITION A custom-built setup for single-molecule localization microscopy is described in [2]. mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample). PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera: exposure time = 100 ms frame size = 512x512 pixels pixel size = 80 nm   <ol> <li>Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.</li> <li>Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073</li> </ol>

Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (CD28-mEos3.2)

This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555) Zip file contains PALM measurements of HEK293 cells expressing CD28 fused with mEos3.2. Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames. Detailed protocols for sample preparation and data acquisition are described in the article. Some details are listed below. SAMPLE PREPARATION cell line: Flp-In™ T-REx™ 293 transfection method: modified calcium-phosphate transient transfection [1] fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperature imaging buffer: PBS PALM ACQUISITION A custom-built setup for single-molecule localization microscopy is described in [2]. mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample). PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera: exposure time = 100 ms frame size = 512x512 pixels pixel size = 80 nm   <ol> <li>Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.</li> <li>Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073</li> </ol>

opencc-by-4.0Sep 2021View details →

Simulations of Single Molecule Localization Microscopy frames with scattered single emitters

Datasets used in the work "Combining deep learning with SUPPOSe and Compressed Sensing for SNR-enhanced localization of overlapping emitters". The file Sample dataset.zip contains simulated images of frames of Single-Molecule Localization Microscopy. In the directory structure, Q is the number of emitters, d is the emitter distance (in pixels), imax is the image maximum intensity and i indexes different noise realizations. There are three images within each folder: X is a noiseless image, Y is the image with noise and background and Z is a denoised image predicted using a convolutional neural network. The file Train dataset.zip contains 5000 simulated pairs of images of single emitters distributed randomly that were used to train a convolutional neural network for denoising. The folder X contains noiseless images and the folder Y contains the corresponding images with noise and background. In all cases, a Gaussian PSF with size \(\sigma = 3\) px was used as the PSF of the imaging system, Noise is modeled as a Poisson process with a dark signal \(i_{dark} = 10\). Corresponding author: Axel M. Lacapmesure (alacapmesure@fi.uba.ar)   CHANGELIST <ul> <li>Version 2: corrected all file extensions in "Train dataset.zip" that were wrong.</li> </ul>

opencc-by-4.0Aug 2021View details →

Dataset for Journal of Applied Physics 130, 124502 (2021) - Force microscopy cantilevers locally heated in a fluid: temperature fields and effects on the dynamics

"Fig7.fig": Matlab figures including all the measured and treated data used to plot figure 7 of the article. "Fig7_data.mat ": Matlab files containing the data to plot figure 7 of the article. "Fig7_plot.m ": Matlab scripts to plot the data of the Matlab files "Fig7_data.mat" "Fig10.fig": Matlab figures including all the measured and treated data used to plot figure 10 of the article. "Fig13.fig": Matlab figures including all the measured and treated data used to plot figure 13 (in the appendix) of the article.

opencc-by-4.0Jan 2022View details →

Dataset for scanning electron microscopy based local fiber volume fraction analysis of non-crimp fabric glass fiber reinforced composites

SEM data sets, Matlab codes, and output from the local fiber volume fraction analysis from the publications: Mortensen, U.A., Rasmussen, S., Mikkelsen, L.P., Fraisse, A., Andersen, T.L. The impact of the fibre volume fraction on the fatigue performance of glass fiber composites used in the wind turbine industry, Composites Part A, submitted Dec 2022. Mikkelsen, Lars P., Fæster, S., Dahl, V.A. Dataset for scanning electron microscopy based local fiber volume fraction analysis of non-crimp fabric glass fiber reinforced composites. Data in Brief, Submitted, 2023. to where a reference should be given.  The files are structured in the following way. <ul> </ul> L1, L2: Low FVF cases 1 and 2; see the publication. H1, H2: High FVF case 1 and 2; see the publication. SEM images: <ul> <li>*.bmp: Single SEM scan</li> <li>*.bmp.hdr: settings for single SEM scan</li> <li>*.tif: Stitched SEM scan</li> <li>*.tif.hdr: settings for stitched SEM scan</li> </ul> *_BundleAnalysis.m: Script for manual segmentation of the individual bundles. <ul> <li>*.zip files: Functions used by the ..._BundleAnalysis.m scripts</li> <li>*-CURVES_AND_AREAS.mat: Matlab saving of bundle definitions used by the ...BUndlesAnalysis.m script</li> <li>*BWbundles.mat: Output from the _BundleAnalysis.m script</li> </ul> *.m: Local fiber volume fraction analysis script of SEM-scan based on output from BundleAnalysis tool <ul> <li>Figxx.png:  Reference to specific figures in the publications shown for all 4 cases</li> <li>Fig7.m: Matlab script for plotting figure 7</li> </ul>

opencc-by-4.0Jun 2023View details →

Label-free adaptive optics single-molecule localization microscopy for whole zebrafish

The specimen-induced aberration has been a major factor limiting the imaging depth of single-molecule localization microscopy (SMLM). Here, we report the application of label-free wavefront sensing adaptive optics to SMLM for deep-tissue super-resolution imaging. The proposed system measures complex tissue aberrations from intrinsic reflectance rather than fluorescence emission and physically corrects the wavefront distortion more than three-fold stronger than the previous limit. This enables us to resolve sub-diffraction morphologies of cilia and oligodendrocytes in whole zebrafish as well as dendritic spines in thick mouse brain tissues at the depth of up to 102 μm with localization number enhancement by up to 37 times and localization precision comparable to aberration-free samples. The proposed approach can expand the application range of SMLM to whole zebrafish that cause the loss of localization points owing to severe tissue aberrations.

dryad36/100

Single-molecule localization microscopy reveals the molecular organization of endogenous membrane receptors

Open the record for dataset details and reuse information.

publicDec 2025View details →

opencc-by-4.0Aug 2024View details →

Data underlying "EVE is an open modular data analysis software for event-based localization microscopy"

Data underlying the manuscript "EVE  is an open modular data analysis software for event-based localization microscopy" Contains raw EBS-recorded SMLM (eveSMLM) data of DNA-PAINT nanoruler, E.coli cell, and aTubulin network in Cos-7 cells (3D and high density acquisitions).

opencc-by-4.0Apr 2024View details →

Localization of protoporphyrin IX in glioma patients with paired stimulated Raman histology and two-photon 3 excitation fluorescence microscopy

<div> <div> <div> <h1>Spatially resolved transcriptomics</h1> Tissue fixation was performed following the ‘Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols’ (CG000160 | Rev C), which included heating the slide and immersing it in pre-chilled methanol. In the tissue staining phase, isopropanol was applied to tissue sections followed by a series of air-drying, hema- toxylin application, washing, bluing buffer application, eosin mix addition, and further washing. The slide was then dried on a heating block. Imaging was conducted using the Evos microscope, with the settings following the previously described protocol. Permeabilization and reverse transcription were undertaken without a preceding tissue optimization on Visium Tissue Optimization Slides, as the optimal permeabiliza- tion time for brain tissue had been established at 12 minutes by a previous researcher. The overall library preparation adhered to the ‘Visium Spatial Gene Expression Reagent Kits – User Guide’ (CG000239 | Rev F). During permeabilization, the Visium slide with stained tissue sections was fitted into a slide cassette and exposed to permeabilization enzyme, followed by a wash with 0.1X SSC buffer. For reverse transcription, an RT master mix was dispensed into each well, followed by a 45-minute incubation period in a thermocycler at 53 ° Celsius. In the second strand synthesis stage, each well received an addition of 75 ul 0.08 M KOH, followed by a brief room-temperature incubation. Subsequently, wells were washed with buffer EB and re- ceived the second strand mix, before undergoing a 15-minute incubation at 65 ° Celsius in a thermocycler. The denaturation process involved washing the wells with buffer EB and adding 35 ul 0.08 M KOH in each well, which were then incubated at room temperature. Afterward, Tris 1 M pH 7.0 was pipetted into four tubes of an 8-tube strip, followed by a transfer of samples from each well into these tubes. The tubes were then vortexed, centrifuged, and placed on ice, with the remaining sample stored for subsequent stages. The experiment initiated with the determination of cycle number wherein a qPCR mix was allocated across five wells of a qPCR plate, with a negative control included. The ensuing qPCR and Cq determination followed the standard protocol used for FFPE methods. Notably, uneven Cq values starting from n.5 were rounded up. In the subsequent cDNA amplification phase, an amplification mix was introduced to each sample tube, followed by thermo-cycling for actual PCR using a specified protocol. The cDNA cleanup process involved adding a SPRIselect reagent to each sample tube, followed by a series of incubation, washing, drying, and buffer addition steps. The cleaned-up samples were then transferred to new tubes. Finally, cDNA quality control and quantification were performed using a Tape Station. The total cDNA yield was calculated, factoring in the library concentration and elution volume. The process of fragmentation, end repair, and A-tailing started with using just a quarter of the purified library, with the remaining portion stored at -20 ° Celsius. The selected volume was mixed with buffer EB and fragmentation mix and incubated in a thermal cycler. Double-sided size selection was performed to discard large fragments and retain fragments within the desired size range. This involved the use of SPRIselect reagent, and resulted in a library with reduced total volume and a smaller range of fragment sizes. Adaptor ligation involved mixing adaptor ligation mix with each sample and incubating in a thermocycler. Post-ligation cleanup followed the cleanup steps post-cDNA amplification, with minor adjustments to the quantities of SPRIselect reagent and buffer EB. Sample index PCR was then performed, with an amp mix and dual index TT set A added to each sample, followed by a specific PCR protocol. The total number of cycles was determined based on the cDNA yield. Another round of double-sided size selection was performed, this time with varied substance quantities, to ensure another cleanup stage. The process concluded with a post-library construction quality control, ensuring the success of the library construction. While no exact concentration calculations were necessary, the fragment size in base pairs was of interest. A Fragment Analyzer was used due to its availability and accuracy in fragment size calculation. Sequencing was performed on a NextSeq 550. <h1>Postprocessing and analysis pipeline</h1> The data analysis and quality control for this research was conducted using the 10X Genomics’ space ranger pipeline and the SPATA2 (version 2.0) framework for spatial data analysis. The SPATA2 object was initiated through the ‘SPATA2::initiateSpataObject_10X’ function. This import procedure involved several stages using the Seurat version 4.0 package. Firstly, gene expression normalization was performed by dividing each spot’s values by the estimated total number of transcripts. These normalized values were then multiplied by 10,000 and underwent a natural logarithm transformation to improve interpretability and comparability across genes. Next, a regression model was applied to remove batch effects and scale the data. This model factored in sample batch and the expression percentages of ribosomal and mitochondrial genes, helping to control for potential sources of unwanted variation in the data. For a more detailed understanding of this process, you can refer to the guide provided at this link: https://themilolab.github.io/SPATA2/. This guide provides comprehensive information about the SPATA2 package and its application in spatial transcriptomics analysis. </div> </div> </div> <div> <div> <div> <h1>Postprocessing and imaging analysis</h1> The H&E images along with the PpIX and SRH images were aligned using afine transformation as described recently. For classification of the PpIX patterns we extracted 160x160 sized patches from each barcode spot and predicted the pattern using the pretrained ResNet architecture. </div> </div> </div>

opencc-by-4.0Dec 2021View details →

Functional Ultrasound Localization Microscopy reveals brain-wide neurovascular activity on a microscopic scale

Matlab script to process fULM dynamic maps and compute activation maps. Two dataset are provided : one from a whiskers stimulation experiment in rats and one from a visual stimulation experiment in rats.

opencc-by-4.0Feb 2022View details →

Determination of protein stoichiometries via dual-color colocalization with single molecule localization microscopy

This entry contains the datasets for the manuscript titled as listed.

opencc-by-4.0Nov 2019View details →

Correcting Artifacts in Single Molecule Localization Microscopy Analysis Arising from Pixel Quantum Efficiency Differences in sCMOS Cameras

Jupyter notebooks and supplementary data for the paper "Correcting Artifacts in Single Molecule Localization Microscopy Analysis Arising from Pixel Quantum Efficiency Differences in sCMOS Cameras".