1,720,983 research outputs found
Fluorescence microscopy videos of mitochondria and endosomes in H9c2 cardiomyoblasts
No full textThis dataset contains a series of three-dimensional fluorescence microscopy videos of the rat cardiomyoblast cell-line H9c2. The outer mitochondrial membrane is labeled with either mCherry (a red fluorescent protein) or eGFP (enhanced green fluorescent protein). Membrane-bound vesicles called endosomes are labeled using mCLING-ATTO647n. A portion of the data is further labeled for acidic vesicles (LysoTracker) and/or has correlative images in brightfield mode (label-free, transmission microscopy). This data is a collection of fluorescence microscopy videos acquired to study the dynamics of mitochondria and the interaction of different subcellular vesicles. Correlative transmission microscopy images (trans) were provided for machine learning to later enable label-free detection of mitochondria and distinguish between different types of vesicles. As three different cameras were used to enable the fast multi-color acquisition, all data has been "channel aligned", i.e., registered to the same sample coordinate system for accurate colocalization of different cellular components. Both unprocessed widefield images and deconvolved data are provided (dimensions: 3D-channels-time) plus maximum intensity z-projected data and AVI-movies of the deconvolved images to enable a quick and easy visualization of the else large image files
Replication Data for: Multiple signal classification as a blind reconstruction approach for three-dimensional structured illumination microscopy
No full textThe dataset contains replication data for the research paper "Multiple signal classification as a blind reconstruction approach for three-dimensional structured illumination microscopy" (3DSIM). The paper compares image reconstructions using conventional 3DSIM and two variants of "Multiple signal classification algorithm" (MUSICAL), MUS-S and MUS-CE.
This dataset provides 1 image generated of mitochondria in living cells, 1 image of mitochondria in fixed cells, 1 image of nephrin in fixed murine kidney tissue using 3DSIM, MUS-S and MUS-CE. The 3DSIM raw data and reconstructions for H9c2 cells are available from https://doi.org/10.18710/PDCLAS.
Four different types of image data are included:
-Raw structured illumination kidney data used for all super-resolution image reconstructions (i.e., MUS-S, MUS-CE and 3DSIM)
-3DSIM images of a kidney section.
-MUS-S for kidney, fixed and live H9c2 cardiomyoblasts
-MUS-CE for kidney, fixed and live H9c2 cardiomyoblasts
The data is organized in different folders according to sample type (FixedCell/LiveCell H9c2, KidneyTissue), and reconstruction method (MUS-CE, MUS-S, 3DSIM).
The image files are TIFF images.
Abbreviations:
3DSIM - three-dimensional structured illumination microscopy
MUSICAL - Multiple signal classification algorithm
MUS-S - soft thresholding variant of MUSICAL
MUS-CE - contrast enhancement, a low-resolution variant of MUSICAL
LTDR - LysoTracker Deep Red
MAX - maximum intensity z-projected three-dimensional images
c or ch - channel<p
Replication Data for: Super-resolution imaging of Schlemm’s canal using 3D-SIM
No full textSeries of three-dimensional structured illumination microscopy (3D SIM) and deconvolution microscopy data of 3µm think tissue sections of Schlemm’s Canal in the chamber angle of mice’s eyes. Schlemm’s Canal endothelium was labeled with an anti-CD31 antibody and an AF647 secondary antibody, the slides were also treated with the nuclear stain DAPI. In addition, eye tissue has significant autofluorescence. The eyes are of either a CD1 mouse strain wildtype animal or of the same background but carrying a βB1-CTGF transgenic construct. CTGF is known to play a key role in mediating the effects of primary open angle glaucoma. The aim of the study was to test the feasibility of 3D SIM of eye tissue and especially in the examination of Schlemm’s Canal
Replication data for: Fluorescence fluctuation-based super-resolution microscopy using multimodal waveguided illumination
No full textThe chip-based total internal reflection fluorescence microscopy data is of fixed salmon keratocytes labelled using phalloidin-ATTO647N and acquired using 660 nm excitation, 10X 0.3NA water dipping objective.
Abstract of publication: Photonic chip-based total internal reflection fluorescence microscopy (c-TIRFM) is an emerging technology enabling a large TIRF excitation area decoupled from the detection objective. Additionally, due to the inherent multimodal nature of wide waveguides, it is a convenient platform for introducing temporal fluctuations in the illumination pattern. The fluorescence fluctuation-based nanoscopy technique Multiple Signal Classification Algorithm (MUSICAL) does not assume stochastic independence of the emitter emission and can therefore exploit fluctuations arising from other sources, as such multimodal illumination patterns. In this work, we demonstrate and verify the utilization of fluctuations in the illumination for
super-resolution imaging using MUSICAL on actin in salmon keratocytes. The resolution improvement was measured to be 2.2–3.6-fold compared to the corresponding conventional images. DHH built the imaging system and contributed in the data acquisition</p
Replication Data for: Physics based machine learning for sub-cellular segmentation in living cells
No full textAbstract:
Segmenting sub-cellular structures in living cells from fluorescence microscopy images is a ground truth (GT) hard problem. The microscope’s 3-dimensional blurring function, finite optical resolution due to light diffraction, finite pixel resolution, and complex
morphological manifestations of the structures, all contribute to GT-hardness. Unsupervised segmentation approaches are quite inaccurate. Manual segmentation relying of heuristics and experience therefore remains the preferred approach. Nonetheless, this process is tedious, with 100s of structures present inside a single cell. Thus, generating analytic across large population of cells or performing advanced artificial intelligence (AI) tasks such as tracking is greatly limited. We bring modeling and deep learning to a nexus for solving this GT-hard problem, improving both the accuracy and speed of sub-cellular segmentation. We introduce the approach of simulation-supervision empowered with physics-based GT. In the simulation-supervision datasets used for training, the physics-based GT resolves the GT hardness while computational modeling of all the relevant physics aspects assists deep learning models to learn to compensate for physics and instrument induced limitations to a great extent. We show extensive results on segmentation of small vesicles and large diversity of mitochondria in diverse independent living and fixed cell datasets, demonstrate the adaptability of the approach across diverse microscopes through transfer learning, and
illustrate biologically-relevant applications of automated analytic and motion analysis
Fluorescence microscopy videos of mitochondria in H9c2 cardiomyoblasts
No full textSeries of three-dimensional fluorescence microscopy videos of the rat cardiomyoblast cell-line H9c2.
Where indicated in the file name, the cells were adapted to galactose (galac). Normal growth conditions are with glucose (gluc).
The outer mitochondrial membranes are labelled with the double tag mCherry-EGFP-OMP-25TM (dTag), i.e., both a red and green fluorescent protein variant.
dTag can be used as a sensor for acidity (or lysosomal degradation), as the green fluorescence is lost sooner in an acidic environment than the red fluorescence.
Where indicated, the samples are additionally labelled with LysoTracker Deep Red (LTDR).
This data is a collection of fluorescence microscopy videos acquired to study the dynamics of mitochondria and the degradation of mitochondria in lysosomes.
Correlative transmission microscopy images (trans) were provided for machine learning to later enable label-free detection of mitochondria and lysosomes.
Each folder contains data from different experimental conditions:
mCh_eGFP_CCCP: mitochondrial outer membrane protein 25 is dually labelled using mCherry-EGFP.
The time-lapses in this folder can be used to study the effect of carbonyl cyanide m-chlorophenyl hydrazone (CCCP) (see more details under methodological information.)
mCh_eGFP_LTDR: mitochondrial outer membrane protein 25 is dually labelled using mCherry-EGFP and acidic compartments using Lysotracker deep red.
mCh_eGFP_LTDR_trans: mitochondrial outer membrane protein 25 is dually labelled using mCherry-EGFP and acidic compartments using Lysotracker deep red. The fluorescence data has correlative label-free brightfield/transmission images (channel 4).
mCh_eGFP_trans: mitochondrial outer membrane protein 25 is dually labelled using mCherry-EGFP.
The fluorescence data has correlative label-free brightfield/transmission images (channel 4)
3DSIM data of mitochondria in the cardiomyoblast cell-line H9c2 adapted to either glucose or galactose
No full textALTERNATIVE DOWNLOAD FROM FileSender:
To access the data via https with limited network capacity, click here.
Series of three-dimensional structured illumination microscopy (3DSIM) of the rat cardiomyoblast cell-line H9c2 adapted to either glucose (GLU) or galactose (GAL).
The outer mitochondrial membranes are labeled with the double tag mCherry-EGFP-OMP-25TM (dTag), i.e., both a red and green fluorescent protein variant. dTag can be used as a sensor for acidity (or lysosomal degradation), as the green fluorescence is lost sooner in an acidic environment than the red fluorescence. Where indicated, the samples are additionally labeled with LysoTracker Deep Red (LTDR).
The aim of the study was to test the feasibility of multi-color 3DSIM for the examination of mitochondria-derived vesicles (MDVs) in both living and fixed cells.</p
Salmon keratocyte DIC microscopy videos
No full textSeries of differential interference contrast microscopy (DIC) videos of primary keratocytes from
Atlantic salmon scales acquired at room temperature (RT).
The salmon from Kårvika (Tromsø Aquaculture Research Station) was about 1 kg +- 0.4 kg of either sex or smolt (about 10 to 15 cm long). The triploid salmon was > 1 kg and from a fish farm at Senja.
The fish and cells were untreated. Unless specifically mentioned, the videos were acquired as single
panels (field-of-view (FOV) 668 µm^2) 5 seconds apart for up to 20 hours, or larger areas (multiple
panels (typically 4 by 4) of a combined FOV 2.7 mm^2) 2 minutes apart for up to 24 hours.
The aim of the study was to investigate salmon skin cell dynamics, which are important to the innate
immunity of fish
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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