Use Case Blob Finder

Measure volumes of cells using the Blob Finder

The Blob Finder analysis operator is ideal for segmenting cells or any other type of rounded cell organelles in a noisy image in an easy-to-use 3-step process.
This new function combines automatic seed finding based on structural information of an object map and a watershed algorithm.
It is part of Analysis Pipeline, which allows for the easy segmentation and subsequent quantitative analysis of cells, spheroids, nuclei or any other type of rounded cell organelles, even in crowded and noisy environments in 2D, 3D and 4D data sets.
This operator can be used without complex image processing beforehand, with integral watershed to correctly split objects even in a densely packed cluster.


Step 1

Measure Diameter

Measure the diameter of the objects of interest

Step 2

Adjust the Threshold

Adjust the Threshold to find the optimal results for segmentation using the preview function for immediate check of the selected parameters.

Step 3

Adjust the Splitting Sensitivity

Adjust the splitting sensitivity to find the optimal results also of densely packed objects.


Results

The Objects Table allows user to calculate various measurements based on the segmented objects. You can highlight individual or groups of objects interactively in the Objects Table and in the 2D and 4D Viewer to do proof reading or closer inspection.
The Objects Table allows to measure and sort by several features such as volume, sphericity, mean fluorescence intensity and many more parameters, including custom features using algebraic combinations of measurements and counts of objects or groups (e.g. ratio of mean intensities two channels).
The measurements can be visualized in the 4D Viewer using a color code (»Use case: Color settings) and exported to Excel or via CSV to any other program for further statistical analysis.

 

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