terewblu.blogg.se - Stereology imagej

#Stereology imagej how to
#Stereology imagej software
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GrainSizeTools script is licensed under the Apache License, Version 2.0 (the "License")

#Stereology imagej license

Journal of Open Source Software, 3(30), 863, License

GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size.

#Stereology imagej how to

How to measure the areas of the grain profiles with ImageJ.

The plot module: visualizing grain size distributions.

Describing the population of grain sizes.

Getting started: first steps using the GrainSizeTools script.

#Stereology imagej download

You can download the script at the following sites:

Two-step method (lognormal fitting, shape characterization).

Stereology methods (approximate the actual 3D grain size distribution from data collected in plane sections):

Histograms and kernel density estimates.

Ready-to-publish plots in bitmap or vector format (see screenshots below), including: It includes multiple piezometric relations for quartz, olivine, calcite, and feldspar (others planned!)

Measures of dispersion and shape of the populationĮstimate differential stress using paleopiezometers.

Estimation of robust confidence intervals (including some specific methods for lognormal populations such as the modified Cox or the GCI method).

Several averages (arithmetic and geometric means, median, and frequency peak ("mode") via Gaussian Kernel Density Estimator).

Import and manipulate tabular-like datasets including txt, csv, or excel formats.įull automatic descriptive statistics of grain size populations including: Latest release: v3.0.2 Date: 1 See notes at Features at a glance

#Stereology imagej code

For users with coding skills, the script is organized in a modular (functional) way facilitating the reuse and code extension. The script does not require previous experience with the Python programming language (see the documentation below and FAQ ). GrainSizeTools is a free, open-source, cross-platform script written in Python that provides tools for (1) describing and visualizing grain size populations, (2) estimating differential stress for different mineral phases via paleopizometers and (3) apply stereology methods to approximate the actual distribution (3D) of grain size from sections.

Lopez-Sanchez - This website was last modified: 3 These results support widespread use of unbiased stereology for analysis of histologic outcomes of injury models.Maintained by Marco A. Automated 2D morphometry overestimated tubular epithelial cell death and correlated modestly with values obtained from unbiased stereology. Unbiased stereology is facilitated by a novel macro for ImageJ and results agree with those obtained using gold-standard methods.

2D morphometry demonstrated poor agreement and significant bias compared to either method of unbiased stereology.Ĭonclusion. There was strong agreement between both methods of unbiased stereology (bias -0.004☐.006 with 95% limits of agreement -0.015 to 0.007). Fluorojade-B stained kidney sections were analyzed using three methods to quantify cell death: gold standard stereology using a controlled stage and commercially-available software, unbiased stereology using the novel ImageJ macro, and quantitative 2D morphometry also using the novel macro. We developed a macro for the widely used image analysis program, Image J, and performed cardiac arrest with cardiopulmonary resuscitation (CA/CPR, a model of acute cardiorenal syndrome) in mice.

#Stereology imagej software

We hypothesized that it would be feasible to build a novel software component which would facilitate unbiased stereologic quantification on scanned slides, and that unbiased stereology would demonstrate greater precision and decreased bias compared with 2D morphometry. Therefore, a challenge to rigorous quantification would be addressed by an unbiased stereology tool with reduced equipment dependence. Histologic sections are commonly analyzed by area morphometry or unbiased stereology, but stereology requires specialized equipment. )Ī technical challenge in translational models of kidney injury is determination of the extent of cell death. Texto completo no disponible (Saber más.Localización: Histology and histopathology: cellular and molecular biology, ISSN 0213-3911, ISSN-e 1699-5848, Vol.