3D volume extraction plugin

[Douglas Benn-2]

I am interested in extracting the 3D volume,  shape and measurements, similar to the output from Analyze, of the sinuses in the face. There are so many plugins available but often with limited description that it is hard to compare them. Can somebody suggest a simple plug for using with thresholded axial CT slices please?


Thank you.


Douglas



Dr Douglas K Benn DDS, PhD, DDR (RCR England)
Professor and Director of Radiology
Creighton University School of Dentistry
Boyne room 207
2802 Webster Street * Omaha NE * 68178

Tel: [phone]

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[SUBSCRIBE IMAGEJ Marie-Laure B]

Hi Douglas,
Perhaps 3d Object counter ?
It's a 3D, black and white image ?

Marie Laure

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[Douglas Benn-2]

Dear Marie,

Yes I have stacks of 16 bit grey level CT images about 444 x 444 x 16 bits. Does it segment 3D volumes and provide geometric and shape data?

I will have a look at this.

Thanks very much.

Douglas



Dr Douglas K Benn BDS, M Phil, DDS, PhD, Diplomate of Dental Radiology (Royal College of Radiologists, England)
Professor and Director of Radiology
Creighton University School of Dentistry
Boyne room 207
2802 Webster Street • Omaha NE • 68178

Tel: [phone]

Confidentiality Notice:

 This e-mail is intended only for the person or entity to which it is
 addressed and may contain information that is privileged, confidential or
 otherwise protected from disclosure. Dissemination, distribution or
  copying of this e-mail or the information herein by anyone other than the
 intended recipient, or an employee or agent responsible for delivering the
 message to the intended recipient, is protected. If you have received
  this e-mail in error, please contact the sender and destroy the original
 message and all copies.





-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of SUBSCRIBE IMAGEJ Marie-Laure B
Sent: Tuesday, November 25, 2014 10:45 AM
To: [hidden email]
Subject: Re: 3D volume extraction plugin

Hi Douglas,
Perhaps 3d Object counter ?
It's a 3D, black and white image ?

Marie Laure

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[SUBSCRIBE IMAGEJ Marie-Laure B]

There is no morphological parameters.
Perhaps this one :
http://www.mecourse.com/landinig/software/software.html

but I didn't test it.
Marie Laure


New in Version 2.0
More parameters are calculated by the plugin (the value -1 indicates that the parameter is no possible to calculate):


    AspRatio: Aspect Ratio = Feret/Breadth,
    Circ: Circularity = 4*Pi*Area/Perimeter2, sometimes called Form Factor or Thinnes ratio. Note that the value is slightly different from that calculated using the built-in Particle Analyzer because of the way the particle area is estimated,
    Roundness: Roundness = 4*Area/(Pi*Feret2),
    AreaEquivD: Area Equivalent Diameter = sqrt((4/Pi)*Area),
    PerimEquivD: Perimeter Equivalent Diameter = Area/Pi,
    EquivEllipseAr: Equivalent Ellipse Area = (Pi*Feret*Breadth)/4, this is the area of an ellipse with the same long and short axes as the particle,
    Compactness: Compactness = sqrt((4/Pi)*Area)/Feret or alternatively ArEquivD/Feret,
    Solidity: Solidity = Area/Convex_Area,
    Concavity: Concavity = Convex_Area-Area,
    Convexity: Convexity = Convex_Hull/Perimeter,
    Shape: Shape = Perimeter2/Area,
    RFactor: RFactor = Convex_Hull /(Feret*Pi),
    ModRatio: Modification Ratio = (2*MinR)/Feret,
    Sphericity: Sphericity = MinR/MaxR,
    ArBBox: ArBBox = Feret*Breadth. This is the area of the Bounding Box along the Feret diameter, but it is not necessarily the minimal bounding box! (Search the net for "rotating calipers algorithm"),
    Rectang: Rectangularity = Area/ArBBox. This approaches 0 for cross-like objects, 0.5 for squares, pi/4=0.79 for circles and approaches 1 for long rectangles.

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