fiji / analyzeskeleton Goto Github PK

ImageJ/Fiji plugin to analyze 2D and 3D skeleton images

Home Page: http://fiji.sc/AnalyzeSkeleton

License: GNU General Public License v3.0

Java 100.00%

analyzeskeleton's Introduction

[ Fiji Is Just ImageJ ]

Fiji is a "batteries-included" distribution of ImageJ—a popular, free scientific image processing application—which includes a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

The main focus of Fiji is to assist research in life sciences.

At the moment, the following platforms are supported:

Windows Intel 32-bit/64-bit
Linux Intel 32-bit/64-bit
MacOSX Intel 32-bit/64-bit (partial support for PowerPC 32-bit)
all platforms supporting Java and a POSIX shell, via bin/ImageJ.sh

The setup is as easy as unpacking the portable archive and double-clicking the ImageJ launcher.

Fiji is intended to be the most painless, easy, quick and convenient way to install ImageJ and plugins and keep everything up-to-date.

Usage

Fiji is meant to be distributed without source, to make the download as small as possible. In the basic version, Fiji is a portable application, i.e. it should run wherever you copy it.

The starting point is the ImageJ launcher, which will launch Java, set up the environment, and call ImageJ.

To pass arguments to ImageJ, just specify them on the command line.

To pass arguments to the Java Virtual Machine, specify them on the command line, separating them from the ImageJ arguments (if any) with a --. In other words, if you want to override the memory setting, call Fiji like this:

$ ./ImageJ-linux32 -Xmx128m --

Open Source

We are dedicated to open source. Not only does open source allow other developers to port the application to new platforms that the original authors did not begin to think of, it allows scientists to study the code to understand the inner workings of the algorithms used, and it permits others to use the program in totally new ways, and enhance it in all imaginable ways.

Therefore, the majority of Fiji is licensed under the GNU Public License version 2. Exceptions are listed in the LICENSES file.

Fiji's source code is split up into a main repository, containing the top-level project and support scripts, while all components live in their own repositories in the Fiji organization on GitHub. As a rule of thumb: the file name and the project name correspond pretty well, e.g. fiji-compat.jar is maintained in fiji-compat.

Participating

Pull Requests are very welcome!

See the Contributing page of the ImageJ wiki.

Authors

Fiji was created by Johannes Schindelin. It is currently maintained by Curtis Rueden of LOCI at the University of Wisconsin-Madison.
ImageJ 1.x was created and is maintained by Wayne Rasband.
ImageJ2 was created and is maintained and actively developed by Curtis Rueden.
For a list of most recent contributors, please refer to the Contributors page of the ImageJ wiki.

Thanks

We are very grateful to Wayne Rasband, who is not only a very dedicated developer of ImageJ 1.x; he also fosters an active and friendly community around ImageJ.

We are especially grateful to be part of an outstanding community who is active, friendly and helping to scientists understanding and analysing images every day.

Oh, and Fiji is also an island. We just wanted to let you know.

analyzeskeleton's People

Contributors

Stargazers

Watchers

Forkers

tferr akatie dongboyan tiabph mathiasunberath bonej-org ralfkeding imageanalysisandprocessing gbyfbi kant mredaelli astuber lahwfb stibnit3 ulypi zhaojk mkynhsn carlos-alberto-silva

analyzeskeleton's Issues

Possible issue in the calculation of the average branch length.

Dear AnalyzeSkeleton developers,

I'm using the latest Fiji release (based on ImageJ 1.51w) on Ubuntu 16.04. The Java version is 1.8.0_171.
I noticed that sometimes the "Average Branch Length" value in is different from the mean of the branch lengths contained in the "Branch information" file.

For example, when processing this image

I obtain the following CSV files:

Branch_information_Batch_aec+af+novegf_merged4.txt

Results_Batch_aec+af+novegf_merged4.txt

At row 6 in the "Results" file, the "Average Brench Length" value is 19.624, while the average of the individual branch lengths, obtained from the "Branch information" file, is 20.478.

Thanks for your useful plugin!

Bug in Analyze Skeleton (2D/3D)

From Fiji BugZilla issue #1164:

when skeletonizing images it can happen that the skeletons are only 1px. I think that the spx and spy values in the Results are not correct. I can´t comment on spy, since I only have 2D data.
The following macro illustrates this.
e.g. spx and spy values in row 4 and 5 are identical. also in row 9 and 10, and ......
run("Blobs (25K)");
run("Make Binary");
run("Skeletonize (2D/3D)");
run("Analyze Skeleton (2D/3D)", "prune=none calculate show");
selectWindow("Results");

Tagged skeleton doesn't show a time axis

When the input skeleton image has a time dimension the tagged skeleton image doesn't show it

Steps to reproduce

Open "mitosis.tif" (File>Open Samples>Mitosis)
Remove channels (Image>Color>Stack to RBG)
Binarise image (Process>Binary>Make Binary)
Run Skeletonize
Run Analyze Skeleton

Calibrated branch length

Hi @iarganda, @hinerm

I'm Angel. How skeleton analyze calculates the calibrated branch length?

Thanks and best regards

Longest Shortest Path Outputs Inconsistent

Hello,

Describe the Bug

The longest shortest path outputs are different across machines. Mainly, there are a different number of rows in each table.

I tested two Windows and one Linux computer running ImageJ 1.53j / Java 1.8.0_172 and they had identical results. Then, I tested two MacOS’s running ImageJ 1.53j / Java 1.8.0_202 and they had different results from the three above and from each other.

Expected Behavior

The outputs should be identical.

Steps to Reproduce

Download and open this image: https://drive.google.com/file/d/1p6jmT2hmJWZToSDhaOGl8-oAX904zqpq/view?usp=sharing
Open Interactive Interpreter and copy and paste the macro (ijm form) below

dir = File.directory;
run("3D Objects Counter", "threshold=50 slice=5 min.=5 max.=134560 objects centroids statistics summary");
selectWindow("Objects map of Substack (36-45).tif");
run("Skeletonize (2D/3D)");
run("Analyze Skeleton (2D/3D)", "prune=[lowest intensity branch] calculate show display original_image=[Substack (36-45).tif]");
selectWindow("Results");
saveAs("Results", dir + "Results" + ".csv");

Run the macro. Output should be where the image is.

Environment & Results

Windows/Linux Results: Results (windows-1.53j, 1.8.0_172).xlsx

ImageJ ver. 1.53j
Java 1.8.0_172
Mean of Longest Shortest Path Excluding Zeros: 7.284857

One of the MacOS Results: Results (macOS-1.53j, 1.8.0_202).xlsx

ImageJ ver. 1.53j
Java 1.8.0_202
Mean of Longest Shortest Path Column Excluding Zeros: 3.380945

Thank you,
Ali

No release version

In the interest of reproducible builds, the pom-fiji parent POM wants to list only release versions. For this to work, there have to be release versions.

@iarganda Mind if I bump this to 2.0.0?

AnalyzeSkeleton can only process 32766 in line 269

Hello,

I am trying to use the DiameterJ plug-in to analyze electrospun fibres and keep receiving this error upon running the plugin.

Can you help me with this issue?

Thanks!

error in analyze skeleton output_Table formatting

Hi
I am having trouble with the data output from Analyse Skeleton and it may have to do with the recent issues with Tables from the recent updates.

It appears that the first column, which is the skeleton id is not appearing and the no of branches ends up being the first column. All the values are shifted by one column, thus reporting the wrong results
I compared this analysis with Analyse skeleton from BoneJ which is included at the bottom of this image.

Cheers
Pradeep