ImageJ Macros

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

The macro segments and classifies human spermatozoids nuclei (DAPI) based on the number of FISH signals (spots) they contain. It reports the percentage of occurrences of user defined classes (combinations of spot multiplicity in the FISH channels) as well as the position (point selections) of the detected nuclei falling in these classes. The input image should be an hyperstack with 4 channels: DAPI (first channel) and three FISH channels. The images are typically obtained as a maximum intensity projection of few channels (confocal) or a single z slice acquisition (widefield).

Example image available in the linked page. 

This macro and plugins suite for ImageJ (and Fiji) serves to measure the velocity of moving structures and visualize them, from image time series (2D over time).

The module can be installed in ImageJ as a Macro Menu and each function/component can be called separately. The full workflow consists in calling some, or all, the functions sequentially in order to get from the image preparation (e.g. filtering and visualization of tracks) to the production of the kymographs (time vs. distance plot) and their analysis (retrieving the velocities).

Here is the full workflow sequence:

• Load image sequence
• Crop and time-filter the image sequence ("Walking average" plugin)
• Generate tracks by z-projection ("Stack difference" plugin)
• Select tracks and restore them in the original stack.
• execute plugin "multiple kymograph"
• Analyse: select edges of moving tracks graphically and quantify movement in a table.

input: 8-bit, 16-bit stacks, 2D in time. Calibrated is better for meaningful velocity measurements.

ouput: the kymograph image, the velocity measurements tables.

Requires ImageJ version: 1.33.n minimum.

Example of applications:

• velocity of moving objects/ structures with sharp edges, incl. the velocity of microtubules (and their plus ends),
• the velocity of vesicles or particles along a 2D path
• the velocity of migration of the edge of a cell or a multicellular group
• retraction velocity of contractile bundles (e.g. actin fibers) or multicellular tissues after mechanical disruption (e.g. laser surgery)

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.