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Image J
Some Image J plugins developed at the CIF.

DocumentsDate added

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file icon Correct X Shifthot! 07/03/2007 Hits: 1183

This plugin is intended to correct the shift that occurs between lines when working with bidirectional acquisition with the LSM 510 confocal microscope.

It can work on any 8-bit image or stack.

The advantage is to be able to do this tuning offline instead of doing it during acquisition.

 

lenaxshift.jpg

file icon Dispose all windowshot! 07/03/2007 Hits: 1188

A small plugin to close all opened windows.

 Useful when associated with a shortcut key. Mandatory if you work with loads of multichannel images which open in seprate windows....Wink

file icon Grid CIFhot! 07/03/2007 Hits: 1217

A modified version of the Grid plugin.

This version allows you to decide the size of the grid based on width and height of the squares and not on the area which can be hard to determine. The grid also starts in the upperleft corner of the image and is no more centered thus reducing the number of non complete squares on the borders.

 

grid.jpg

 

 

file icon G Ratio Calculatorhot! 10/30/2008 Hits: 1815
G Ratio Calculator allows you to calculate the G ratio in the following way:
gratio.jpg 
Image processing

The two first steps (“Prepare image” and “Start measurements”) involve several filters and processing procedures. Then the actual measurement occurs.

Prepare Image
• Convert the image to 8-bit: we do not need color information.
• Apply a median filter: removes noise and allows better edge detection.
• Apply a user-defined threshold: we need to binarize the image.

Start measurements
• Apply an “Open” binary operation on the image: removes residual gaps between “attached” fibers.
• Listen the image for cursor location

Measure
• Auto-outline the inner part of the fiber
• Measure inner area and inner perimeter (a1 and p1)
• Find the border
• Auto-outline the outer part of the fiber
• Measure total area and outer perimeter (a2 and p2)

- Methods used for G factor calculation:

Two values are computed:

pgfactor, which is the perimeter-based g factor, is calculated this way:

pgfactor =  pratio.jpg

agfactor, which is the area-based g factor, is calculated this way:

agfactor =  aratio.jpg

pgfactor and agfactor are totally equal for an ideal round fiber. The more the fiber is distorted, the more these values will differ. If you should use only one of these values, the agfactor should be chosen because it is shape independent.