Employing an open-source tool to assess astrocyte tridimensional structure

Abstract

Astrocytes display important features that allow them to maintain a close dialog with neurons, ultimately impacting brain function. The complex morphological structure of astrocytes is crucial to the role of astrocytes in brain networks. Therefore, assessing morphologic features of astrocytes will help provide insights into their physiological relevance in healthy and pathological conditions. Currently available tools that allow the tridimensional reconstruction of astrocytes present a number of disadvantages, including the need for advanced computational skills and powerful hardware, and are either time-consuming or costly. In this study, we optimized and validated the FIJI-ImageJ, Simple Neurite Tracer (SNT) plugin, an open-source software that aids in the reconstruction of GFAP-stained structure of astrocytes. We describe (1) the loading of confocal microscopy Z-stacks, (2) the selection criteria, (3) the reconstruction process, and (4) the post-reconstruction analysis of morphological features (process length, number, thickness, and arbor complexity). SNT allows the quantification of astrocyte morphometric parameters in a simple, efficient, and semi-automated manner. While SNT is simple to learn, and does not require advanced computational skills, it provides reproducible results, in different brain regions or pathophysiological states.

Activated mesenchymal stem cell administration inhibits chronic alcohol drinking and suppresses relapse‐like drinking in high‐alcohol drinker rats

“…Total length and thickness of primary processes of astrocytes were assessed for six GFAP positive cells per Z‐stack according to Tavares et al . ().…”

Blockade of microglial adenosine A2A receptor suppresses elevated pressure‐induced inflammation, oxidative stress, and cell death in retinal cells

“…Iba‐1 immunoreactive cells were evaluated from four human donors, in a total of 21–28 cells analyzed per condition. Microglia reconstruction was performed using Simple Neurite Tracer open source software from Fiji‐ImageJ, available at (http://fiji.sc/Simple_Neurite_Tracer:_Step-By-Step_Instructions; ), as previously described (Tavares et al, ). From this analysis, the morphologic parameters assessed were a total number of processes, total length, last intersection radius, and Sholl analysis.…”

Intranasal Administration of Mesenchymal Stem Cell Secretome Reduces Hippocampal Oxidative Stress, Neuroinflammation and Cell Death, Improving the Behavioral Outcome Following Perinatal Asphyxia

“…The area inspected for each stack was 0.04 mm 2 and the thickness (Z-axis) was measured for each case. The total lengths of primary and secondary processes for six IBA-1 positive cells per Z-stack were analyzed by three-dimensional reconstruction using the Simple Neurite Tracer plugin of FIJI image analysis ( ) [ 103 ] following the protocol described by Tavares et al [ 104 ].…”