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97 results for “laser scanning microscopy”
Fluorescent Confocal Laser Scanning Microscopy of White Blood Cells, Cancer Cell Line MCF7, and Mixtures of these Cells: A Model System for Circulating Tumor Cell Biomarker Evaluation V.1
<p>This is a confocal laser scanning microscopy data set of white blood cells (leukocytes), the cancer cell line MCF7, and mixtures of these cells acquired on a Zeiss LSM 780 microscope in the University of Colorado Anschutz Medical Campus Advanced Light Microscopy Core. Cells are fluorescently labeled for DNA with DAPI (Sigma D9542), lipids with Bodipy 495/503 (Thermo Fisher D3922), the filament protein cytokeratin (CK) with pan-cytokertain-alexa555 antibodies (Cell Signaling Technologies 3478S) and the surface membrane antigen CD45 with CD45-alexa647 antibodies (Biolegend 304020). Bodipy was excited with a continuous wave (CW) 488 nm laser, alexa555 was excited with CW 561 nm laser, and alexa647 was excited with a CW 633 nm laser. The acquiring instrument does not have a CW 405 nm source so DAPI was excited by two photon process using a Coherent Cameleon ultrafast pulsed laser tuned to 765 nm. The objective used was a Zeiss Plan-Apochromat 20x, 0.8 NA, air.</p> <p>The data consists of 4 channel 8x8 mosaic z-stacks. The Zeiss software performed stitching of the mosaics. These stitched data images are included and marked with _Stitched at the end. Those interested in performing the stitching themselves can do this with the raw data files (without the _Stitched). The jpeg images are processed from the stitched LSM images. The LSM files contain additional meta data on the experiment including power levels and acquisition settings.</p> <p>The _Stiched .lsm files will load in ImageJ (tested with V.1.49) as 4 channel 3 stack images.</p> <p>This data is a model system for evaluating the DNA/Lipids/CK/CD45 biomarker panel to identify circulating tumor cells (CTCs). The D- population of the model is the WBCs and the D+ population is the MCF7 cancer cell line. The amount of separation the biomarker panel plus analysis algorithm can produce between these populations (D+/D-) is an estimate the sensitivity and specificity of the biomarker panel plus algorithm to CTCs.</p> <p>Experiments generating the data were performed over the course of 15 days. Peripheral blood samples were collected from the Gynecological Tissue and Fluid Bank (COMIRB 07-0935 / COMIRB 05-1081) from consenting patients undergoing surgery at the University of Colorado Hospital. Blood samples were used the same day they were collected. Blood samples were collected from 3 patients with benign conditions, labeled WBBN#, and 3 patients with ovarian cancer, labeled WBCA#. We do not expect there to be any difference in the isolated white blood cells samples prepared from the cancer and benign patients. Samples were stored at room temperature until white blood cells were isolated. Mixed samples were prepared by passaging a MCF7 flask and mixing it with isolated white blood cells before fixation. A schedule showing the time duration between collection, processing and imaging is included as “experimental schedule.gif”.</p> <p>The MCF7 cancer cell line was a kind gift from Dr. Heide Ford. Genomic DNA was isolated from the MCF7 cell line after the experiment and sent for cell line authentication. The gDNA was a match to MCF7. The authentication report and data are included in this submission.</p> <p>CD45 antibodies were exhausted on day 7. New antibody was purchased and received on day 8. The day 7 images only has labels for DAPI and Bodipy. The samples prepared with the old antibodies on days 4 and 7 were relabeled and imaged with the new antibodies on days 14 and 15. This labeling was also done to confirm the pan-CK antibodies remained good since they are dim in the MCF7 cells imaged on days 12 and 13. The pan-CK on days 14 and 15 looks the same as it did on days 5 and 7 confirming the antibodies are good.</p> <p>Four of the filters containing cells were not sufficiently flat to be acquired with a 3 slice z-stack so a 5 slice z-stack was used. These files have been zipped to compress them under the 2 GB limit permitted by zenodo.org</p> <p>Further information on how these samples were prepared, processed, and analyzed can be found in our associated 2016 SPIE Photonics West BIOS conference proceeding titled, “Quantitative image cytometry measurements of lipids, DNA, CD45 and cytokeratin for circulating tumor cell identification in a model system”, http://dx.doi.org/10.1117/12.2222317.</p> <p>This work was supported by funding provided to the University of Colorado Cancer Center by the American Cancer Society and awarded as Institutional Research Grant Number 57-001-53, by funding provided by the Defense Advanced Research Projects Agency under grant number N66001-10-4035, and by funding provided by NIH/NCATS Colorado CTSI Grant Number TL1 TR001081. The University of Colorado Anschutz Medical Campus Advanced Light Microscopy Core is also supported in part by NIH/NCATS Colorado CTSI Grant Number UL1 TR001082. The funders had no role in the study design, data collection, analysis, or decision to publish.</p>
Metadata for Confocal Laser Scanning Microscopy Images of Monoculture and Mixed-Species Biofilms Formed by Bacterial Isolates of Dairy Origin
<p>In a project conducted by ILVO (Belgium), a wide variety of bacterial species were recovered from the surface of a dairy pasteurizer after cleaning and disinfection (C&D). The biofilm-forming ability of these bacteria was determined in both single-species and various mixed-culture combinations. Some work related to this study has been published in Frontiers: "Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries". Bacterial species were mixed in different combinations to assess the community biofilm mass and growth dynamics of individual species. ILVO and the University of Copenhagen conducted experiments aimed at revealing the structural characteristics and spatial organization of bacterial species within different mixed-species biofilms. In our research, we employed oligonucleotide FISH probes, each conjugated with a unique fluorescent dye: Cy5 for <em>Stenotrophomonas rhizophila</em> (B68), Cy3 for <em>Bacillus licheniformis</em> (B65), and FAM for <em>Microbacterium lacticum</em> (B30). C1 combination refers to a combination containing B68 and B30. </p> <p><span>Images of the biofilms formed on the coupons were captured using a confocal laser scanning microscope (LSM 800, Zeiss) with a Plan-Apochromat 63x/1.4 oil-immersion objective. Z-stacks were recorded to obtain three-dimensional (3D) images. Standard images were made with an image size of 1024 × 1024 pixels, corresponding to physical dimensions of 101.4 × 101.4 μm for each image. For each image, two separate channels were applied to detect any dual-species combination using a flexible detector (GaAsP-PMT) in the LSM 800 system. Representative 3D views of images were generated using the 3D model function in the ZEN system 3.7.</span></p> <p>Biofilms were grown in BHI for 24 h on plastic coupons. The samples were imaged at different time points: 6h, 12h, 18h and 24h. Each samples had three replicates and for each replicate imaging was performed from 3-6 different positions. </p> <p>Details of the oligonucleotide probes are given below:</p> <table> <tbody> <tr> <td> <p><strong><span>Name of the species</span></strong></p> </td> <td> <p><strong><span>Sequences</span></strong></p> </td> <td> <p><strong><span>Max. excitation</span></strong></p> </td> <td> <p><strong><span>Max. emission</span></strong></p> </td> <td> <p><strong><span>Fluorophores</span></strong></p> </td> </tr> <tr> <td> <p><em><span>S. rhizophila</span></em><span> B68<span> </span></span></p> </td> <td> <p><span>GGGCCTTTACCCCGCCA</span></p> </td> <td> <p><span>649 nm</span></p> </td> <td> <p><span>670 nm</span></p> </td> <td> <p><span>Cy5</span></p> </td> </tr> <tr> <td> <p><em><span>B. licheniformis</span></em><span> B65</span></p> </td> <td> <p><span>ACCGCCTGCGCGCGCTT</span></p> </td> <td> <p><span>550 nm</span></p> </td> <td> <p><span>570 nm</span></p> </td> <td> <p><span>Cy3</span></p> </td> </tr> <tr> <td> <p><em><span>M. lacticum</span></em><span> B30</span></p> </td> <td> <p><span>CCCCACCCTTTCGCTCC</span></p> </td> <td> <p><span>495 nm</span></p> </td> <td> <p><span>520 nm</span></p> </td> <td> <p><span>FAM</span></p> </td> </tr> </tbody> </table>
FIG. 4 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 4. — Confocal tomographies of the reproductive system of Brachylaima mazzantii (Travassos, 1927): A, Mehlis' gland (mg), vitelline reservoir (vr), ovary (ov) and testes (t); B, ovary (ov), seminal reservoir (sr), testes (t) and intestinal caeca (ic); C, ovary (ov) and ootype (oo); D, vitelline glands (vg) forming lobed acini; E, vitelline duct (vd) showing vitelline cells inside forming a single row; F, uterus full of eggs; G, egg, revealing the embryo (emb), eggshell (sh), operculum (op) and discontinuity area (da) in the eggshell. Scale bars: A, B, D, F, 50 μm; C, E, 10 μm; G, 5 μm.
FIG. 8 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 8. — Reproductive system of Brachylaima mazzantii (Travassos, 1927) as first described by Travassos in 1927 (adapted from Lent & Freitas 1937). Scale bar: 1 mm.
FIG. 1 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 1. — Confocal tomographies of the reproductive system of Brachylaima mazzantii (Travassos, 1927): A, gland cells (gc) surrounding the genital pore (gp); B, commissure (co) and gland cells (gc); C, region of the genital opening showing differentiated musculature (dfm); D, female genital opening (fgo), male genital opening (mgo) and unarmed cirrus (ci); E, cirrus pouch (cip), metraterm (m), testes (t), bursa (b) and seminal vesicle (sv); F, vitelline duct (vd), vitelline reservoir (vr), uterus (u), ovary (ov) and testes (t). Scale bars: 50 μm.
FIG. 6 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 6. — Confocal tomographies of tegument, musculature of the body and acetabulum of Brachylaima mazzantii (Travassos, 1927): A, tegument covered by many scales; B, scales; C, circular musculature (cm); D, longitudinal (lm) and diagonal musculature (dm); E, two differentiated muscle bundles (dfm); F, surface of acetabulum featuring many papillae (p); G, papillae (p), radial musculature (rm) and differentiated musculature (dfm) supporting the acetabulum; H, papillae. Scale bars: A-G, 50 μm; H, 10 μm.
FIG. 3 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 3. — Schematic drawings of the reproductive system of Brachylaima mazzantii (Travassos, 1927): A, reconstruction of the reproductive system from the confocal tomographies, showing seminal vesicle (sv), metraterm (m), cirrus (c), cirrus pouch (cp), genital atrium (ga), testes (t), ovary (o), ootype (oo), vitelline duct (vd), vitelline glands (vg) vitelline reservoir (vr), and Mehlis' gland (mg); B, cirrus pouch as first described by Travassos in 1927 (adapted from Lent & Freitas 1937). Scale bars: A, 0.06 mm; B, 0.25 cm.
FIG. 5 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 5. — Confocal tomographies showing the anterior region of Brachylaima mazzantii (Travassos, 1927): A, image showing the meridional musculature (mm); B, equatorial musculature (eqm); C, radial musculature (rm), papillae (p) on the surface of the oral sucker and differentiated musculature (dfm) making the transition between mouth and pharynx (pre-pharynx); D, pharynx (ph), radial musculature (rm), esophagus (e), and intestinal caeca (ic); E, detail of the intestinal caeca, revealing numerous microvilli (mi), and the epithelium (ep); F, esophageal glands (eg) circling the esophagus. Scale bars: A-D, 50 μm; E, 10 μm.
FIG. 2 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 2. — Schematic drawings of the genital atrium of Brachylaima mazzantii (Travassos, 1927): A-D, sequential tomographic images starting from the body surface. Scale bar: 5 µm.
FIG. 7 in New insights on the morphology of a digenean parasite Digenea: Brachylaimidae, Brachylaima mazzantii (Travassos, 1927)) using confocal laser scanning microscopy
FIG. 7. — Confocal tomographies of the excretory and nervous system of Brachylaima mazzantii (Travassos, 1927): A, excretory ducts (exd), testes (t); B, excretory bladder (exb), excretory pore (exp), and testes (t); C, longitudinal nervous cord (nc); D, commissures (co) originated from the nervous cord (nc). Scale bars: A-C, 50 μm; D, 10 μm.
V79 fibroblasts loaded with 50 nm PVP coated gold particles captures by confocal laser scanning microscopy
<p>Data was recorded continuously in a region of 41x41 μm² at a scan rate of 1400 Hz resulting in a frame duration of 94 ms; the pinhole was set to 600 μm (5.778 μm layer), image resolution was 256x256 pixel. (11 FPS)</p>
Scan tiles obtained through Confocal Laser Scanning Microscopy for roughness characterization of surfaces
<p>The Data includes all the original data collected from individual scan tiles of both quartz and glass surfaces using Confocal Laser Scanning Microscopy. The techniques used for merging scan tiles linearly, as well as the procedures for data processing and analysis, are detailed in the methods and results sections of this manuscript. A sperate methods section include along with data files also describe the details of the Image acquisition, preprocessing, and tiling methodology.</p>
Data from: Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy
<p>This repository contains the raw data of the experimental ISM dataset used to make the figures and supplementary figures for the paper entitled <em>Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy.<br></em></p>
Dynamic deformation calculation of articular cartilage and cells using resonance-driven laser scanning microscopy - Deformable Registration Validation Dataset
<p>This dataset includes the supporting input files, scripts, and output files for validation tests of lsmgridtrack v0.3 applied to resonance scanned images. </p>
FIGURE 53 in Re-description of Chinese mitten crab Eriocheir sinensis H. Milne Edwards, 1853 (Crustacea: Brachyura: Grapsoidea: Varunidae) zoeal development using confocal laser scanning microscopy
FIGURE 53. An example measurement of dorsal, lateral and rostral spines using a ZI stage of Cancer magister (adapted from Shirley et al. 1987).
FIGURE 50 in Re-description of Chinese mitten crab Eriocheir sinensis H. Milne Edwards, 1853 (Crustacea: Brachyura: Grapsoidea: Varunidae) zoeal development using confocal laser scanning microscopy
FIGURE 50. Eriocheir sinensis, ZVI, second maxilliped, CLSM images with Drishti processing. (A) coxa, basis and endopod, applying "large images" option with a scanned area of 1×2 fields for image stitching, (B) endopod with 0,1,7 setae, (C) exopod with 13 natatory setae. Objective: 20× dry. Scale bars A, C = 500 µm; B = 100 µm.
FIGURE 45 in Re-description of Chinese mitten crab Eriocheir sinensis H. Milne Edwards, 1853 (Crustacea: Brachyura: Grapsoidea: Varunidae) zoeal development using confocal laser scanning microscopy
FIGURE 45. Eriocheir sinensis, ZVI, antenna, CLSM images with Drishti processing. (A) antenna with apparent 2-articled endopod distal tip almost equal to length of protopod, applying "large images" option with a scanned area of 1×2 fields for image stitching, (B) antenna with endopod slightly shorter than length of protopod, image merged using Adobe Photoshop. Objective: A = 20× dry; B = 40× oil immersion. Scale bars = 200 µm.
FIGURE 42 in Re-description of Chinese mitten crab Eriocheir sinensis H. Milne Edwards, 1853 (Crustacea: Brachyura: Grapsoidea: Varunidae) zoeal development using confocal laser scanning microscopy
FIGURE 42. Eriocheir sinensis, ZV, CLSM images with Drishti processing. (A) dorsal view of pleon and telson, (B) lateral view of pleon and telson; both applying "large images" option with a scanned area of 2×3 fields for image stitching, (C) pleomere 1 with 7 medial setae, (D) dorsal view of telson showing a pair of medial setae. Objective: A-B = 10× dry; C-E =20× dry. Scale bars = 500 µm.
FIGURE 43 in Re-description of Chinese mitten crab Eriocheir sinensis H. Milne Edwards, 1853 (Crustacea: Brachyura: Grapsoidea: Varunidae) zoeal development using confocal laser scanning microscopy
FIGURE 43. Eriocheir sinensis, ZVI, CLSM images with Drishti processing. (A) general view of ventral carapace margin with a much shorter lateral spine, (B) ventral carapace margin detailed, (C) dorsal spine with 4 pairs of setae; all applying "large images" option with a scanned area of 2×3 fields for image stitching. Objective: 20× dry. Scale bars = 500 µm.
FIGURE 41 in Re-description of Chinese mitten crab Eriocheir sinensis H. Milne Edwards, 1853 (Crustacea: Brachyura: Grapsoidea: Varunidae) zoeal development using confocal laser scanning microscopy
FIGURE 41. Eriocheir sinensis, ZV, CLSM images with Drishti processing. (A) third maxilliped, applying "large images" option with a scanned area of 1×2 fields for image stitching, (B) pereiopods with bilobed chela, (C) ventral view of fifth pleopods with endopods and uropods without endopods; both applying "large images" option with a scanned area of 2×2 fields for image stitching. Objective: 20× dry. Scale bars A = 100 µm; B-C = 500 µm.
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Allen Brain Atlas
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International Brain Laboratory public data
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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.