Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 138671, Singapore.
Published: June 2011
AI Article Synopsis
Article Abstract
Background: Image segmentation is a crucial step in quantitative microscopy that helps to define regions of tissues, cells or subcellular compartments. Depending on the degree of user interactions, segmentation methods can be divided into manual, automated or semi-automated approaches. 3D image stacks usually require automated methods due to their large number of optical sections. However, certain applications benefit from manual or semi-automated approaches. Scenarios include the quantification of 3D images with poor signal-to-noise ratios or the generation of so-called ground truth segmentations that are used to evaluate the accuracy of automated segmentation methods.
Results: We have developed Gebiss; an ImageJ plugin for the interactive segmentation, visualisation and quantification of 3D microscopic image stacks. We integrated a variety of existing plugins for threshold-based segmentation and volume visualisation.
Conclusions: We demonstrate the application of Gebiss to the segmentation of nuclei in live Drosophila embryos and the quantification of neurodegeneration in Drosophila larval brains. Gebiss was developed as a cross-platform ImageJ plugin and is freely available on the web at http://imaging.bii.a-star.edu.sg/projects/gebiss/.
Background: Oligodendroglial development is accompanied by increased cell complexity. A simple and cost-effective evaluation of the pro-myelinating activity of different drugs and/or treatments would be of great interest. In cultured oligodendroglia, an evaluation of the pro-myelinating activity of different drugs and/or treatments can be achieved through fractal analysis, which allows measuring cell complexity.
Background And Aims: Colony-stimulating factor 1 (CSF1) is a growth factor secreted by dorsal root ganglia (DRG) neurons important for DRG macrophages and spinal cord (SC) microglia injury-induced proliferation and activation, specifically released after spared nerve injury (SNI). In this study, we investigated if SNI-induced CSF1 expression and perineuronal rings of macrophages around mouse DRG neurons vary between L3-L5 DRG and with the neuronal type, and if the CSF1 neuronal projections at the SC dorsal horns were associated with an increased microglial number in the corresponding laminae.
Methods: Seven days after surgery, L3-L5 DRG as well as their corresponding segments at the SC level were collected, frozen, and cut.
Oxidative stress has been implicated in several chronic pathological conditions, leading to cell death and injury. Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM) have several overlapping mechanisms as they are both characterized by increased oxidative stress, inflammation, insulin resistance, and autophagy dysfunction. The objective of this study was to elucidate the possible neuroprotective effect of empagliflozin, a sodium-glucose co-transporter 2 inhibitor (SGLT2i), against hydrogen peroxide-induced neurotoxicity in primary hippocampal neurons derived from wild-type (WT) and transgenic AD rats (TgF344-AD).
Live cell imaging is a robust method to visualize dynamic cellular structures, especially organelles with network-like structures such as mitochondria. In this regard, mitochondrial dynamics, namely mitochondrial fission and fusion, are highly dynamic processes that regulate mitochondrial size and morphology depending on a plethora of cellular cues. Likewise, lysosome size and distribution may hint at their function and state.
Cells have unique structural patterns that can reveal important information about their functions, but detecting these patterns manually in large datasets is difficult and biased.
The Structural Repetition Detector (SReD) is a new computational tool that automatically identifies these repetitive structures using local texture similarity, without requiring prior knowledge about the images.
SReD has been tested on various microscopy images and has proven useful for studying neural structures, HIV-1 assembly, and microtubule dynamics, with an open-source plugin available for wider use in biological research.
