fiji / correct_3d_drift

[ 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.

correct_3d_drift's Issues

Feature Request: Restrict shifts to x and y dimension

Hi there,
I really like this tool and I use it in one of my projects.
I deal with movies, that are acquired in fixed z-stacks, which don't drift. However, the plugin sometimes detects a z-shift and corrects it, which then messes up the rest of the down-stream processing, where I combine several movies.
It would be great if there was an option to restrict the shifts to x and y dimensions instead of fixing the file output of the virtual processing afterwards.
Whether you implement it or not, thanks anyway :)
Julia

Using Correct_3d_drift on .tif files

I have .tif files captured on a field of view of mouse brain using 2d photon microscopy. There is no time axis for now. Each frame in the .tif file represents the tissue at a depth 'z'. These frames are not aligned properly. Can i use your tool to align such frames?

result image shown twice

The result images was shown twice in a sense that the imp.show() command was occurring two times in the code. In GUI usage this did not matter, but it appears that when running the script from within and IJ macro with setBatchMode( true ) there are two result images, which apparently leads to erroneous behaviors (reported by user on IJ Forum).
I removed the second imp.show().

@ctrueden: Could you release the new version?

Unable to apply pre-computed vectors

Thank you for the tool, I was unable to find a way (either in FIJI forum searches or the documentation) to apply the pre-computed vectors, is there an intended way to do it?

make citeable in ZENODO

@ctrueden @acardona @imagejan @robertb-r
Someone approached me about how to cite the Correct_3D_Drift plugin...

I could make it cite-able via ZENODO. I did that already for a couple of other plugins:
https://zenodo.org/deposit?page=1&size=20
What do you think?
Of course we could use another (shared) ZENODO account for this rather than my private one.

Refactor Point3f to simply array

The current code contains unnecessary Point3f java objects, which make it overly complicated.
Would be much simpler to have 3D arrays.
For example, code like below could be replaced by loops or even on-liners:

    minx = min(minx, shift.x)
    miny = min(miny, shift.y)
    minz = min(minz, shift.z)