MultiMap: A Tool to Automatically Extract and Analyse Spatial Microscopic Data From Large Stacks of Confocal Microscopy Images

Abstract

The development of 3D visualization and reconstruction methods to analyse microscopic structures at different levels of resolutions is of great importance to define brain microorganization and connectivity. MultiMap is a new tool that allows the visualization, 3D segmentation and quantification of fluorescent structures selectively in the neuropil from large stacks of confocal microscopy images. The major contribution of this tool is the posibility to easily navigate and create regions of interest of any shape and size within a large brain area that will be automatically 3D segmented and quantified to determine the density of puncta in the neuropil. As a proof of concept, we focused on the analysis of glutamatergic and GABAergic presynaptic axon terminals in the mouse hippocampal region to demonstrate its use as a tool to provide putative excitatory and inhibitory synaptic maps. The segmentation and quantification method has been validated over expert labeled images of the mouse hippocampus and over two benchmark datasets, obtaining comparable results to the expert detections.

RETRACTED: NeuroSuites: An online platform for running neuroscience, statistical, and machine learning tools

“…• MultiMap (Figure 3J), an extensible application to deal with large stacks of confocal microscopic images at different levels of resolutions (Varando et al, 2018). The possibility of creating regions of interest (of any shape and size) is a great advantage of the tool.…”

Distribution of GABAergic Neurons and VGluT1 and VGAT Immunoreactive Boutons in the Ferret (Mustela putorius) Piriform Cortex and Endopiriform Nucleus. Comparison With Visual Areas 17, 18 and 19

“…A recent study using a Gaussian filter and an automated object detection process reported a new approach to a fast and accurate 3D analysis of fluorescent puncta in the neuropil of large brain areas, avoiding the more tedious deconvolution procedure (Varando et al, 2018). In our study, we used the deconvolution procedure for the analysis of 2D confocal images, which gives also an accurate bouton quantification to define the inhibitory profile of the ferret visual cortex.…”

Quantitative Image Analysis for Tissue Biomarker Use: A White Paper From the Digital Pathology Association

“…Although image analysis exists for these applications, they are much less advanced compared with WSI. [9][10][11]…”

“…For example, microscopy with UV surface excitation imaging relies on illuminating unstained tissues with UV light at wavelengths <300 nm, which allows visualization of cellular properties in tissues with similar information content to H&E stains, but without the need for fixation and processing. Although image analysis exists for these applications, they are much less advanced compared with WSI 9–11…”