Image Scanning Microscopy
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This document discusses image scanning microscopy (ISM), a technique that improves the resolution and contrast of fluorescence microscopy images. ISM works by acquiring multiple images of the sample from different positions and combining them to generate a single image with effectively doubled resolution. The document outlines the basic principles and components of ISM systems, provides examples of applications like imaging fluorescent beads and cell structures, and discusses related techniques for further enhancing resolution and depth of imaging. It concludes by emphasizing ISM's benefits like high resolution, low photodamage, and multicolor imaging capabilities.
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Part 2 of 2 of lecture series introducing undergraduate neuroscience students to the core electrophysiological and imaging techniques used to study neuronal activity.
A UGMENT R EALITY IN V OLUMETRIC M EDICAL I MAGING U SING S TEREOSCOPIC...
This document discusses using stereoscopic 3D displays to view volumetric medical imaging data in augmented reality. It summarizes an experiment that tested how three factors - convergence, accommodation, and relative size - affect depth perception when viewing 3D medical images on a stereoscopic display. The experiment found that convergence and accommodation significantly impacted depth perception, while relative size had a negligible effect. Viewing images between 227-291mm in front of the screen provided the most effective depth perception.
Statistical Feature-based Neural Network Approach for the Detection of Lung C...
Lung cancer, if successfully detected at early stages, enables many treatment options, reduced risk of invasive surgery and increased survival rate. This paper presents a novel approach to detect lung cancer from raw chest X-ray images. At the first stage, we use a pipeline of image processing routines to remove noise and segment the lung from other anatomical structures in the chest X-ray and extract regions that exhibit shape characteristics of lung nodules. Subsequently, first and second order statistical texture features are considered as the inputs to train a neural network to verify whether a region extracted in the first stage is a nodule or not . The proposed approach detected nodules in the diseased area of the lung with an accuracy of 96% using the pixel-based technique while the feature-based technique produced an accuracy of 88%.
Spatial Laser Induced Fluorescence Imaging (SLIFIMG) Analysis to Assess Tissu...
Fluorescence technique involves the optical detection and spectral analysis of light emitted by a substance undergoing a transition from an excited electronic state to a lower electronic state. The aim of this study is to assess the -amino levulinic acid (-ALA) uptake. Based on image processing technique, Matlab was used to analyze the fluorescence images resulted from activation of (-ALA) and follow its uptake along one week. Analyzing the RGB colours pixel profile from obtained results showed different profiles for malignant tissues, normal tissues, treated just after PDT and finally at one week post PDT. The treated tissues fluorescence profile showed changes from closer to malignant tissue profile till been closed to normal one.
uantitative Morphometric Analysis of Immunochemistry Images of the Spinal Dor...
uantitative Morphometric Analysis of Immunochemistry Images of the Spinal Dor...ANALYTICAL AND QUANTITATIVE CYTOPATHOLOGY AND HISTOPATHOLOGY
This study introduces a new quantitative analysis technique for evaluating immunohistochemistry images of the spinal dorsal horn (SDH) in a rat model of chronic neuropathic pain. Eight rats underwent a spinal cord dorsal hemisection injury to induce neuropathic pain. Immunofluorescent staining for NeuN and GABA was performed on spinal cord sections. A novel ellipse region of interest was defined based on the distribution of NeuN-positive neurons to standardize measurements between samples. This technique showed a significant loss of GABAergic neurons and decrease in GABA immunoreactivity in deeper regions of the injured SDH compared to the uninjured side. This method allows for quantitative comparison of cell distributions and immunoreactivity intensities in the SDH.Determination ofRadiological Quality Parameters Using Optical Densitometer an...
This study determined radiological quality parameters using an optical densitometer and simple fabricated equipment. A wooden step wedge and metal pin were exposed to x-rays and their optical densities were measured. The results showed that simple fabricated equipment can determine parameters like dose, beam alignment, peak kilovoltage and tube current consistency without specialized quality control equipment. Optical density was directly proportional to factors like kilovoltage, tube charge and dose. Beam alignment was within acceptable limits. Therefore, simple fabricated devices can be used to establish quality protocols and monitor parameters in areas lacking quality control testing equipment.
Biophysics by the sea 2016 program and abstract book
Biophysics by the sea 2016 program and abstract book
International conference on fluorescence super-resolution microscopy, spectroscopy, molecular cell mechanics and theoretical neurophysics
26th. -30th. september 2016
Pollentia resort, Alcudia, Spain
Event organizer:
Georg August University
Third Institute of Physics
Dirk Hähnel
37077 Göttingen
Augmented Reality in Volumetric Medical Imaging Using Stereoscopic 3D Display
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Measuring visual acuity and contrast sensitivity by optomotor reflex in rodents
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In this webinar, sponsored by Striatech and supported in part by Stoelting, researchers will present objective and bias-free results obtained using a newly developed automated optomotor system. For more information, please visit: https://insidescientific.com/webinar/measuring-visual-acuity-contrast-sensitivity-optomotor-reflex-striatech
Ghent University Global Campus - Sungkyunkwan University: Workshop on Researc...
Ghent University Global Campus - Sungkyunkwan University: Workshop on Research and Academic Development
Analysis of microscope images_FINAL PRESENTATION
This document outlines the presentation scheme for a thesis on the analysis of microscope images. The thesis will analyze tissue samples using both polarimetric imaging at a macroscopic level and microscope imaging at a cellular level. For polarimetric imaging, the thesis will develop statistical models to characterize tissue properties based on how polarized light interacts with tissue elements. For microscope imaging, it will automatically segment cells from immunohistochemistry images and evaluate biomarkers like Her2 to characterize cancer impacts. Key techniques will include membrane boundary estimation, image clustering, and watershed transforms. The goal is both material characterization from polarimetric signatures and cancer analysis from cellular-level microscope images.
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Use of spatial frequency domain imaging (sfdi) to quantify drug delivery
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A UGMENT R EALITY IN V OLUMETRIC M EDICAL I MAGING U SING S TEREOSCOPIC...
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Biophysics by the sea 2016 program and abstract book
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Augmented Reality in Volumetric Medical Imaging Using Stereoscopic 3D Display
Augmented Reality in Volumetric Medical Imaging Using Stereoscopic 3D Display
Measuring visual acuity and contrast sensitivity by optomotor reflex in rodents
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Ghent University Global Campus - Sungkyunkwan University: Workshop on Researc...
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More from Dirk Hähnel
DFG Advanced Microscopy Workshop Wuerzburg 2011
1. Image scanning microscopy (ISM) is a fluorescence microscopy technique that enhances spatial resolution approximately twofold compared to confocal laser scanning microscopy (CLSM).
2. ISM works by combining focused laser excitation with wide-field detection using an EMCCD camera. Images are taken at various scan positions of the excitation focus and combined to form a higher resolution composite image, similar to structured illumination microscopy (SIM).
3. ISM has advantages over SIM in that it is more robust against optical aberrations and imperfections since it does not require patterned illumination. The ISM setup can acquire super-resolution 3D multi-color images and optionally modulate excitation intensity for further resolution gains from non-linear effects
20th. Single Molecule Workshop Picoquant 2014
SIMA is a novel software tool that enables automated single-molecule spectroscopy experiments on surface-immobilized molecules. It locates target molecules, plans an optimal measurement procedure by configuring detector exposure, excitation events, and position control. SIMA then executes the measurements by navigating through the sample space and controlling the positioning system in real-time for each molecule position. This allows complex measurements to be conducted with ease while saving time and minimizing photobleaching compared to manual experiments. As a demonstration, SIMA was used to simultaneously measure the three-dimensional orientation of the absorption and emission dipoles of single fluorescing molecules by combining point spectroscopy with localized wide-field imaging.
20th. Single Molecule Workshop Picoquant 2014
Embedded Environments for Confocal Spinning Disc Image-Scanning Microscopy (CSDISM) and Superresolution Optical Fluctuation Imaging (SOFI)
BIOS 2015 San Francisco
Dirk Hähnel presented on making image scanning microscopy and stochastic optical fluctuation imaging (SOFI) more user-friendly. Key challenges include keeping the price below $10,000 USD, making the tools accessible to physicists, chemists, and other users, and reducing artifacts in image stacks of dynamic biological systems. The talk discussed developing easy-to-use software plugins for MicroManager, improving calibration and acquisition speed, and hardware for fast image reconstruction. Roadmaps were presented for integrating these improvements into beta software by mid-2015 to enable double resolution and simplify use of the complex techniques.
SOFI Developer Meeting Göttingen 28th March 2015
Vistas for hardware implementation of SOFI: High speed imaging for rapid biological processes Imaging fast, user-friendly and integrate with ease
21st International Workshop on “Single Molecule Spectroscopy and Super-resolu...
Filling the usability gap: Bioinformatics solutions for Image-Scanning Microscopy, Stochastic Optical Fluctuation Imaging, and Surface Single Molecule Experiments
HPC and HPGPU Cluster Tutorial
Short and comprehensive manual to extend your local matlab with a high performance computing cluster of NVidia tesla's 2070 graphical processing units.
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Image Scanning Microscopy
- 1. Image Scanning Microscopy Dirk Hähnel - Group Seminar 30.04.2013 III. Institute of Physics – Biophysics Georg-August-University Göttingen Göttingen 30.05.2013
- 2. Problem 2 Göttingen 30.05.2013
- 3. 3 Diffraction Göttingen 30.05.2013
- 4. Methods Schermelleh et.al, JCB 4 Göttingen 30.05.2013
- 5. 5 System Overview Göttingen 30.05.2013
- 6. 6 Data Acquisition Göttingen 30.05.2013
- 7. 7 Image Information Y_Sample Each pixel acts like a small confocal aperture for a two-dimensional Göttingen 30.05.2013 image X_Sample X_CCD Y_CCD
- 8. 8 Image Processing Each CCD pixel acts as nearly infitly small pinhole Superimpose of al pixel from all images, the resulting image is blurred, due to parrallax effect Reshifting image in common reference frame results in sharp image with ~doubled resolution Göttingen 30.05.2013
- 9. 9 Results ●Fluorescent bead imaging ●Increase of contrast and resolution Intensity profile of a single fluorescent bead *scalebar indicates 1 mm Quedlinburg 26th Sep. 2011
- 10. 10 Increase Resolution Using saturation of the excited state Taking measurements on at least two different intensity-levels Archiving the higher harmonic in the Fourier-space Quedlinburg 26th Sep. 2011
- 11. 11 Optical Saturation Microscopy Confocal Image Optical Saturation Microscopy Image Yeast cell with GFP-labeled Ato1p membrane protein ,J. Humpolickova, A. Benda and J. Enderlein, Biophys. Journal, 2009 (97), 2623–2629. Quedlinburg 26th Sep. 2011
- 12. 12 Deep Tissue with Olympus Scaleview: 2Photon Göttingen 30.05.2013 Hiroshi Hama, Hiroshi Kurokawa, Hiroyuki Kawano, Ryoko Ando,Tomomi Shimogori, Hisayori Noda, Kiyoko Fukami, Asako Sakaue-Sawano & Atsushi Miyawaki "Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain," Nature Neuroscience, advance online publication, 30 August 2011
- 13. 13 Faster ISM CLSM & MPM Göttingen 30.05.2013
- 14. 14 Software Development and Standards • CSDISM Plugin for Fiji/Imagej – Acquisition: Java wrapper Labview – Post processing: Java Plugin Imagej /BioFormat et.al System Biology Göttingen 30.05.2013
- 15. 15 Conclusion • ISM – Image Scanning Microscopy – Any Dye – Multicolor – Low Intensity/ Damage – 3D • Resolution enhancement DSOM • FAST ISM – Super High Resolution <100k€ • 2Photon Deep Tissue • Software Tools for System Biology Community (STANDARDS) Göttingen 30.05.2013
- 16. 16 Acknowledgements Göttingen 30.05.2013