A simple optical tissue clearing pipeline for 3D vasculature imaging of the mediastinal organs in mice.

Optical tissue clearing (OTC) methods render tissue transparent by matching the refractive index within a sample to enable three-dimensional (3D) imaging with advanced microscopes. The application of OTC method in mediastinal organs in mice remains poorly understand. Our aim was to establish a simple protocol pipeline for 3D imaging of the mediastinal organs in mice.

Application of ethyl cinnamate based optical tissue clearing and expansion microscopy combined with retrograde perfusion for 3D lung imaging.

Purpose: 3 D imaging of the lung is not a trivial undertaking as during preparation the lung may collapse. Also serial sections and scans followed by 3 D reconstruction may lead to artifacts. The present study aims to figure out the best way to perform 3 D imaging in lung research.

New technical approaches for 3D morphological imaging and quantification of measurements.

3D imaging is becoming more and more popular, as it allows us to identify interactions between structures in organs. Furthermore, it gives the possibility to quantify and size these structures. To allow 3D imaging, the tissue sample has to be transparent.

Bioreactor for mobilization of mesenchymal stem/stromal cells into scaffolds under mechanical stimulation: Preliminary results.

Introduction: Articular cartilage (AC) is a viscoelastic tissue with a limited regenerative capability because of the lack of vasculature. Mechanical stimulation contributes to the homeostasis of functional AC since it promotes the delivery of nutrients, cytokines and growth factors between the distant chondrocytes. We hypothesized that biomechanical stimulation might enhance mobilization of endogenous mesenchymal stem/stromal cells (MSCs) from neighboring niches as the bone marrow.

Transcutaneous Measurement of Glomerular Filtration Rate in Rodents.

Glomerular filtration rate (GFR) is considered the gold standard to test kidney function. However, the serial blood and/or urine sample collection required for the calculation of the GFR is stressful for the animal and time consuming for the experimenter. Here, we describe a transcutaneous assessment of renal function in conscious animals that does not require plasma or urine sampling and/or deep anesthesia.

A cationic near infrared fluorescent agent and ethyl-cinnamate tissue clearing protocol for vascular staining and imaging.

Understanding vascular structures and dysfunction is a fundamental challenge. This task has been approached by using traditional methodologies such as microscopic computed tomography and magnetic resonance imaging. Both techniques are not only expensive but also time-consuming.

AutoCellSeg: robust automatic colony forming unit (CFU)/cell analysis using adaptive image segmentation and easy-to-use post-editing techniques.

In biological assays, automated cell/colony segmentation and counting is imperative owing to huge image sets. Problems occurring due to drifting image acquisition conditions, background noise and high variation in colony features in experiments demand a user-friendly, adaptive and robust image processing/analysis method. We present AutoCellSeg (based on MATLAB) that implements a supervised automatic and robust image segmentation method.

A New Feedback-Based Method for Parameter Adaptation in Image Processing Routines.

The parametrization of automatic image processing routines is time-consuming if a lot of image processing parameters are involved. An expert can tune parameters sequentially to get desired results. This may not be productive for applications with difficult image analysis tasks, e.

A Benchmark Data Set to Evaluate the Illumination Robustness of Image Processing Algorithms for Object Segmentation and Classification.

Developers of image processing routines rely on benchmark data sets to give qualitative comparisons of new image analysis algorithms and pipelines. Such data sets need to include artifacts in order to occlude and distort the required information to be extracted from an image. Robustness, the quality of an algorithm related to the amount of distortion is often important.