Measure Stack

Measure Stack

Author: Bob Dougherty

Installation: Download (Measure_Stack.class, MeasureStack.class, and MeasureStackReviewer.class) or Measure_Stack.java to the plugins folder.

Description: A plugin to perform measurements on a series of distinct ROIs in the slices of a stack. The results are summed to determine the volume of a 3D object and the mean gray value of pixels within the object. The plugin may have applications to movies, as well as 3D stacks.
The ROI exists on a range of consecutive slices. The user creates the ROI on key slices. The plugin interpolates the ROI for the slices in between the key slices. Linear interpolation is used. Any slice upon which the user creates an ROI becomes a key slice. A slice can be make non-key by removing the ROI. Slices before the first slice with an ROI and after the last slice with an ROI are not included in the measurements.
The measurements can be restricted by setting limits in Image>Adjust>Threshold... In this way, the total volumes of 3D particles within the ROI can be found.

Instructions: Open a stack containing a 3D object. Choose Measurement options in Analyze>Set Measurements.... "Area" and "Mean Gray Value" should usually be included. Run (or Compile and Run...) Measure_Stack. To measure a volume, find the first slice that includes part of the object, and create an ROI of the perimeter in this slice. Advance to the slice with the largest part of the object and create an ROI around that. Find the last slice with part of the object and make an ROI. The plugin will automatically create ROIs on the intermediate slices, but they may not be good fits to the object. Find the slice with the worst fit. "Review areas" or Image>Stacks>Start Animation may be helpful for the inspection. Correct the ROI with the worst fit and continue the process until the match is satisfactory for all of the slices. Press "Measure" on the Measure_Stack control panel. If desired, the measurement options and/or the ROIs can be changed, and Measure can be repeated.
Notes:

Use the "Slice Spacing" control to enter the distance between the slices. The computed volume is proportional to this value.

The ROI type must be the same on all slices with selections. "Choosing" with a different ROI tool removes all of the old ROIs.

Multiple ROIs on a single slice are not supported.

Interpolated ROIs are shown in red. User-drawn (key) ROIs are yellow. (Sometimes they are red while being drawn.)

When making polygon selections, always go around the same direction (clockwise or counterclockwise) and start at about the same angle.

If you do not require different ROIs on different slices (usually because the threshold can do all the work), try Voxel Counter.

Special Version: Define the ROI on one stack and measure a different stack with Measure Stacks. Download (Measure_Stacks.class, MeasureStacks.class, and MeasureStackReviewer.class) or Measure_Stacks.java to the plugins folder.

Versions: 0: 6/12/2002 Beta release.
1: 6/24/2002 The close box works. Slice numbers are listed in the results. The "Review areas" button was added. Interpolated ROIs are red.

Open items: Find the overall modal value.
Find the overall standard deviation.
(Option) determine surface areas.

License:
Copyright (c) 2002, 2005, OptiNav, Inc.
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

Neither the name of OptiNav, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ImageJ: ImageJ can be freely downloaded from the ImageJ web site.

Author:	Bob Dougherty
Installation:	Download (Measure_Stack.class, MeasureStack.class, and MeasureStackReviewer.class) or Measure_Stack.java to the plugins folder.
Description:	A plugin to perform measurements on a series of distinct ROIs in the slices of a stack. The results are summed to determine the volume of a 3D object and the mean gray value of pixels within the object. The plugin may have applications to movies, as well as 3D stacks. The ROI exists on a range of consecutive slices. The user creates the ROI on key slices. The plugin interpolates the ROI for the slices in between the key slices. Linear interpolation is used. Any slice upon which the user creates an ROI becomes a key slice. A slice can be make non-key by removing the ROI. Slices before the first slice with an ROI and after the last slice with an ROI are not included in the measurements. The measurements can be restricted by setting limits in Image>Adjust>Threshold... In this way, the total volumes of 3D particles within the ROI can be found.
Instructions:	Open a stack containing a 3D object. Choose Measurement options in Analyze>Set Measurements.... "Area" and "Mean Gray Value" should usually be included. Run (or Compile and Run...) Measure_Stack. To measure a volume, find the first slice that includes part of the object, and create an ROI of the perimeter in this slice. Advance to the slice with the largest part of the object and create an ROI around that. Find the last slice with part of the object and make an ROI. The plugin will automatically create ROIs on the intermediate slices, but they may not be good fits to the object. Find the slice with the worst fit. "Review areas" or Image>Stacks>Start Animation may be helpful for the inspection. Correct the ROI with the worst fit and continue the process until the match is satisfactory for all of the slices. Press "Measure" on the Measure_Stack control panel. If desired, the measurement options and/or the ROIs can be changed, and Measure can be repeated. Notes: Use the "Slice Spacing" control to enter the distance between the slices. The computed volume is proportional to this value. The ROI type must be the same on all slices with selections. "Choosing" with a different ROI tool removes all of the old ROIs. Multiple ROIs on a single slice are not supported. Interpolated ROIs are shown in red. User-drawn (key) ROIs are yellow. (Sometimes they are red while being drawn.) When making polygon selections, always go around the same direction (clockwise or counterclockwise) and start at about the same angle. If you do not require different ROIs on different slices (usually because the threshold can do all the work), try Voxel Counter.
Special Version:	Define the ROI on one stack and measure a different stack with Measure Stacks. Download (Measure_Stacks.class, MeasureStacks.class, and MeasureStackReviewer.class) or Measure_Stacks.java to the plugins folder.
Versions:	0: 6/12/2002 Beta release. 1: 6/24/2002 The close box works. Slice numbers are listed in the results. The "Review areas" button was added. Interpolated ROIs are red.
Open items:	Find the overall modal value. Find the overall standard deviation. (Option) determine surface areas.
License:	Copyright (c) 2002, 2005, OptiNav, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of OptiNav, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
ImageJ:	ImageJ can be freely downloaded from the ImageJ web site.