Image segmentation

This macro performs measurements of average and standard deviation intensity inside wells of a protein microarray (the number of wells is limited to 250, the image should be cropped for larger arrays). The macro requires the "ImageJ plugins toolkit". To ensure compatibility with Fiji you should download the version 1.6.1. The installation instructions can be found here, it only consists in un-compressing the .jar file from the previous archive to Fiji plugins folder.

sample image: link

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This pipeline shows how to identify smaller objects (foci) within larger objects (nuclei) and how to use the Relate module to establish a relationship between the two as well as perform per-object aggregate measurements (such as number of foci per nucleus). Sample images are included in the download package.

Simple workflow description for ImageJ, step-by-step description for delineating focal adhesions, count and characterize their positions.  

Measurement of dynamics is not involved.

This macro is meant to segment the cells of a multicellular tissue. It is written for images showing highly contrasted and uniformly stained cell membranes. The geometry of the cells and their organization is automatically extracted and exported to an ImageJ results table. This includes: Cell area, major, minor fitted ellipse radii + major axis orientation and number of neighbors of the cells. Manual correction of the automatic segmentation is supported (merge split cells, split merged cells).

Sample image data is available in the documentation page. 

Simple macro to separates blobs.

• Load the ImageJ sample image "Blobs"
• Run the plugin Morphological Segmentation
• Display the overlaid

This macro depends on "Morphological Segmentation" component of the MorphoLibJ library, which should be installed via update sites.