Measurements using a low-resolution atlas: Once worms are untangled, this pipeline shows how they can be straightened and aligned with a low-resolution worm atlas to extract localized intensity measurements and compare patterns of reporter If adjusting the pipeline to fit your own data, worm detection will likely improve by creating a new worm model based Untangling requires a worm model, which is provided together with the pipeline.
elegans and extract measurements on a per-worm basis. WormToolbox These pipelines have been developed for high-throughput screens onĬ. To measure the degree of overlap between two fluorescent channels. This example shows how the object identifcation and RelateObjects modules are used Measure the degree of spatial coincidence and potential interactions among subcellular species (e.g., proteins). Colocalization: Measuring the colocalization between fluorescently labeled molecules is a widely used approach to.This example shows how the CorrectIlluminationCalculate and CorrectIlluminationApply modules are used to compensate for the non-uniformities in illumination often Illumination Correction: Illumination correction is often important for both accurate segmentationĪnd for intensity measurements.Rather than identifying individual cells, this pipeline quantifies Wound Healing: In this example, cells are grown as a tissue monolayer.
#Tophat method cellprofiler how to
How to input a color tissue image, split it into its component channels, and then identify individual cells from a particular stain and record the number of neighbors that each cell has. Tissue Neighbors: Tissue samples often have irregularly shaped cells with adjacent edges.To the grid defintion and identification modules.
#Tophat method cellprofiler Patch
Percentage of stained objects: CellProfiler is commonly used to count cells or other objects as well as percent-positives, by measuring the per-cell staining intensity. Cell/particle counting, and scoring the.Specialized pipelines In addition to cellular object and feature identification, these pipelines include some of the more specialized modules in CellProfiler for image pre-processing or measurement. Of DNA contained in the tail is calculated. Also shown is a silver-stained comet example in which the percentage Also, illumination correction is used to reduce background flourescence prior to measurement. The length and intensity of the comet tail.
Comet assay This is a simple example of a DNA damage assay using single cell gel electrophoresis.Tumors: A simple pipeline that identifies and counts tumors in a mouse lung, and then measures their size.Pipeline demonstrates how to identify these clumpy cells and obtain morphological, intensity and texture measurements. Fruit fly cells: In comtrast to the HT29 cells, Drosophila Kc167 cells are a highly textured and clumpy cell type.This pipeline demonstrates how to accurately identify theseĬells and how to measurements cellular parameters such as morphology, count, intensity and texture. Human cells: Human HT29 cells are fairly smooth and elliptical.Basic Pipelines These pipelines are made for simple cellular and tissue image assays, and include some basic measurements.