Estimating object number in biological structures

Scaling up cell-counting efforts in neuroscience through semi-automated methods

Quantifying how the cellular composition of brain regions vary across development, aging, sex, and disease, is crucial in experimental neuroscience, and the accuracy of different counting methods is continuously debated. Due to the tedious nature of most counting procedures, studies are often restricted to one or a few brain regions. Recently, there have been considerable methodological advances in combining semi-automated feature extraction with brain atlases for cell quantification. Such methods hold great promise for scaling up cell-counting efforts. However, little focus has been paid to how these methods should be implemented and reported to support reproducibility. Here, we provide an overview of practices for conducting and reporting cell counting in mouse and rat brains, showing that critical details for interpretation are typically lacking. We go on to discuss how novel methods may increase efficiency and reproducibility of cell counting studies. Lastly, we provide practical recommendations for researchers planning cell counting.

Basic quantitative morphological methods applied to the central nervous system

Generating numbers has become an almost inevitable task associated with studies of the morphology of the nervous system. Numbers serve a desire for clarity and objectivity in the presentation of results and are a prerequisite for the statistical evaluation of experimental outcomes. Clarity, objectivity, and statistics make demands on the quality of the numbers that are not met by many methods. This review provides a refresher of problems associated with generating numbers that describe the nervous system in terms of the volumes, surfaces, lengths, and numbers of its components. An important aim is to provide comprehensible descriptions of the methods that address these problems. Collectively known as design-based stereology, these methods share two features critical to their application. First, they are firmly based in mathematics and its proofs. Second and critically underemphasized, an understanding of their mathematical background is not necessary for their informed and productive application. Understanding and applying estimators of volume, surface, length or number does not require more of an organizational mastermind than an immunohistochemical protocol. And when it comes to calculations, square roots are the gravest challenges to overcome. Sampling strategies that are combined with stereological probes are efficient and allow a rational assessment if the numbers that have been generated are "good enough." Much may be unfamiliar, but very little is difficult. These methods can no longer be scapegoats for discrepant results but faithfully produce numbers on the material that is assessed. They also faithfully reflect problems that associated with the histological material and the anatomically informed decisions needed to generate numbers that are not only valid in theory. It is within reach to generate practically useful numbers that must integrate with qualitative knowledge to understand the function of neural systems.

Human TAUP301L overexpression results in TAU hyperphosphorylation without neurofibrillary tangles in adult zebrafish brain

Microtubule-associated TAU protein is a pathological hallmark in Alzheimer's disease (AD), where hyperphosphorylation of TAU generates neurofibrillary tangles. To investigate the effects of TAU in a regenerative adult vertebrate brain system, we generated a cre/lox-based transgenic model of zebrafish that chronically expresses human TAUP301L, which is a variant of human TAU protein that forms neurofibrillary tangles in mouse models and humans. Interestingly, we found that although chronic and abundant expression of TAUP301L starting from early embryonic development led to hyperphosphorylation, TAUP301L did not form oligomers and neurofibrillary tangles, and did not cause elevated apoptosis and microglial activation, which are classical symptoms of tauopathies in mammals. Additionally, TAUP301L neither increased neural stem cell proliferation nor activated the expression of regenerative factor Interleukin-4, indicating that TAUP301L toxicity is prevented in the adult zebrafish brain. By combining TAUP301L expression with our established Aβ42 toxicity model, we found that Aβ42 ceases to initiate neurofibrillary tangle formation by TAUP301L, and TAUP301L does not exacerbate the toxicity of Aβ42. Therefore, our results propose a cellular mechanism that protects the adult zebrafish brain against tauopathies, and our model can be used to understand how TAU toxicity can be prevented in humans.

Quantitative assessment of angiogenesis, perfused blood vessels and endothelial tip cells in the postnatal mouse brain

During development and in various diseases of the CNS, new blood vessel formation starts with endothelial tip cell selection and vascular sprout migration, followed by the establishment of functional, perfused blood vessels. Here we describe a method that allows the assessment of these distinct angiogenic steps together with antibody-based protein detection in the postnatal mouse brain. Intravascular and perivascular markers such as Evans blue (EB), isolectin B4 (IB4) or laminin (LN) are used alongside simultaneous immunofluorescence on the same sections. By using confocal laser-scanning microscopy and stereological methods for analysis, detailed quantification of the 3D postnatal brain vasculature for perfused and nonperfused vessels (e.g., vascular volume fraction, vessel length and number, number of branch points and perfusion status of the newly formed vessels) and characterization of sprouting activity (e.g., endothelial tip cell density, filopodia number) can be obtained. The entire protocol, from mouse perfusion to vessel analysis, takes ∼10 d.

Local estimators of size in stereological studies

There are two general categories of stereological methods, global and local. Global stereological estimators include estimators of total volume, surface, length, and number. Local estimators can be used to estimate the volumes or surfaces of single objects and, thereby, the distribution of object sizes or the mean size of objects within a population. Two local estimators that have proved to be of practical value for measuring the volume of cells in neurobiological studies are the nucleator and the rotator, which are the focus of this article. Variants of the nucleator can be used for estimating object number, object surface, and the spatial distributions of objects.

Counting and measuring ultrastructural features of biological samples

Ultrastructural features of cells can be fractions of a micrometer in diameter, and electron microscopy is needed to resolve them to a degree that is compatible with stereological techniques. Because the focal depth of transmission electron microscopy (TEM) images is thousands of times greater than the thickness of the sections used with TEM, virtual sectioning of sections suitable for TEM is not possible, as it is with light microscopy and the optical disector probe. With features the size of neuronal synapses, for example, this necessitates the use of physical sections and physical disectors. Regardless of how the imaging is performed, the design of stereological studies for quantifying ultrastructural features will be essentially the same as that used in the example described here, which uses physically separated ultrathin sections viewed with conventional TEM to estimate the number and size of synapses in a particular brain region.