163 research outputs found
Model-Based Cell Tracking and Analysis in Fluorescence Microscopy
Biological research is impossible to imagine without a microscope. Latest genera-
tions of microscopes, able to produce huge arrays of multidimensional data, only
distantly resemble Leeuwenhoek’s first microscope. Every advance in visualization
techniques and hardware brings us one step closer to understanding life, e.g., how
genome information gives identity to cells, how cells constitute organisms and how
errant cells cause disease. Discovery of the green fluorescent protein (GFP) in the nineties of the previous century was definitely one of the most impor-
tant milestones on that path, giving new strong impulse to the field of fluorescence
microscopy
Stochastic neighbor embedding as a tool for visualizing the encoding capability of magnetic resonance fingerprinting dictionaries
Objective To visualize the encoding capability of magnetic resonance fingerprinting (MRF) dictionaries. Materials and methods High-dimensional MRF dictionaries were simulated and embedded into a lower-dimensional space using t-distributed stochastic neighbor embedding (t-SNE). The embeddings were visualized via colors as a surrogate for location in low-dimensional space. First, we illustrate this technique on three different MRF sequences. We then compare the resulting embeddings and the color-coded dictionary maps to these obtained with a singular value decomposition (SVD) dimensionality reduction technique. We validate the t-SNE approach with measures based on existing quantitative measures of encoding capability using the Euclidean distance. Finally, we use t-SNE to visualize MRF sequences resulting from an MRF sequence optimization algorithm. Results t-SNE was able to show clear differences between the color-coded dictionary maps of three MRF sequences. SVD showed smaller differences between different sequences. These findings were confirmed by quantitative measures of encoding. t-SNE was also able to visualize differences in encoding capability between subsequent iterations of an MRF sequence optimization algorithm. Discussion This visualization approach enables comparison of the encoding capability of different MRF sequences. This technique can be used as a confirmation tool in MRF sequence optimization.Radiolog
On the ability to exploit signal fluctuations in pseudocontinuous Arterial Spin Labeling for inferring the major flow territories from a traditional perfusion scan
Neuro Imaging Researc
Biosensor Cell-Fit-HD4D for correlation of single-cell fate and microscale energy deposition in complex ion beams
We present a protocol for the biosensor Cell-Fit-HD4D. It enables long-term monitoring and correlation of single-cell fate with subcellular-deposited energy of ionizing radiation. Cell fate tracking using widefield time-lapse microscopy is uncoupled in time from confocal ion track imaging. Registration of both image acquisition steps allows precise ion track assignment to cells and correlation with cellular readouts. For complete details on the use and execution of this protocol, please refer to Niklas et al. (2022)
Transcriptomic signatures associated with regional cortical thickness changes in Parkinson's disease
Cortical atrophy is a common manifestation in Parkinson's disease (PD), particularly in advanced stages of the disease. To elucidate the molecular underpinnings of cortical thickness changes in PD, we performed an integrated analysis of brain-wide healthy transcriptomic data from the Allen Human Brain Atlas and patterns of cortical thickness based on T1-weighted anatomical MRI data of 149 PD patients and 369 controls. For this purpose, we used partial least squares regression to identify gene expression patterns correlated with cortical thickness changes. In addition, we identified gene expression patterns underlying the relationship between cortical thickness and clinical domains of PD. Our results show that genes whose expression in the healthy brain is associated with cortical thickness changes in PD are enriched in biological pathways related to sumoylation, regulation of mitotic cell cycle, mitochondrial translation, DNA damage responses, and ER-Golgi traffic. The associated pathways were highly related to each other and all belong to cellular maintenance mechanisms. The expression of genes within most pathways was negatively correlated with cortical thickness changes, showing higher expression in regions associated with decreased cortical thickness (atrophy). On the other hand, sumoylation pathways were positively correlated with cortical thickness changes, showing higher expression in regions with increased cortical thickness (hypertrophy). Our findings suggest that alterations in the balanced interplay of these mechanisms play a role in changes of cortical thickness in PD and possibly influence motor and cognitive functions.Neuro Imaging Researc
Image registration and mutual thresholding enable low interimage variability across dynamic MRI measurements of supraclavicular brown adipose tissue during mild cold exposure
Purpose: Activated brown adipose tissue (BAT) enhances lipid catabolism and improves cardiometabolic health. Quantitative MRI of the fat fraction (FF) of supraclavicular BAT (scBAT) is a promising noninvasive measure to assess BAT activity but suffers from high scan variability. We aimed to test the effects of coregistration and mutual thresholding on the scan variability in a fast (1 min) time-resolution MRI protocol for assessing scBAT FF changes during cold exposure. Methods: Ten volunteers (age 24.8 +/- 3.0 years; body mass index 21.2 +/- 2.1 kg/m(2)) were scanned during thermoneutrality (32 degrees C; 10 min) and mild cold exposure (18 degrees C; 60 min) using a 12-point gradient-echo sequence (70 consecutive scans with breath-holds, 1.03 min per dynamic). Dynamics were coregistered to the first thermoneutral scan, which enabled drawing of single regions of interest in the scBAT depot. Voxel-wise FF changes were calculated at each time point and averaged across regions of interest. We applied mutual FF thresholding, in which voxels were included if their FF was greater than 30% FF in the reference scan and the registered dynamic. The efficacy of the coregistration was determined by using a moving average and comparing the mean squared error of residuals between registered and nonregistered data. Registered scBAT Delta FF was compared with single-scan thresholding using the moving average method. Results: Registered scBAT Delta FF had lower mean square error values than nonregistered data (0.07 +/- 0.05% vs. 0.16 +/- 0.14%; p09150161910073Metabolic health: pathophysiological trajectories and therap
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