The number and volume of glomeruli are very important for the diagnosis and treatment of various kidney diseases¹^,²^,³^,⁴^,⁵. The golden standard of glomeruli number estimation is the physical dissector/fractionator combination. However, this method requires special reagents and equipment, making it slow and expensive⁶^,⁷^,⁸^,⁹. Biopsy provides a wealth of information, but obviously, this method is only suitable for rough estimations¹⁰^,¹¹. Medical imaging technologies, including magnetic resonance imaging (MRI), computed tomography (CT), and X-ray, are also widely used in glomerular detection¹²^,¹³^,¹⁴^,¹⁵, but such technologies require bulky instruments. New methods, such as matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometer¹⁶ or the thick and thin section method¹⁷, have also been used in glomerular detection, though they remain tedious and laborious.

With the help of transparency technologies, it is possible to observe deeper depths and obtain richer and more complete information from thick tissues or even whole organs¹⁸^,¹⁹^,²⁰^,²¹^,²²^,²³. Therefore, transparency technologies have been widely used in kidney research²⁴. The observation and detection of glomeruli in the cleared kidneys are also involved. However, these published articles either only briefly referred to glomerular detection²⁵ or used difficult-to-achieve labeling methods such as transgenic animals²⁶, self-produced dyes¹³, or high-concentration antibody incubation²⁷ to label the glomeruli. In addition, although studies had analyzed glomeruli in cleared kidneys, the analyses were always limited¹³ or relied on analysis algorithms established by the authors themselves²⁶.

We have previously demonstrated a more convenient way to label the glomeruli in mice kidneys²⁸. By using Imaris, we found that glomeruli count, frequency, and volume could be quickly obtained. Thus, here we present a more accessible, comprehensive, and simplified set of methods to label and analyze the glomeruli of mice kidneys.

Data Processing and Quantification of Glomeruli from Microscopy Images