fiji / cookbook

Plugins collated for the Fiji Cookbook

cookbook's Issues

Nucleus counter modes not functional

Working with 8 bit grayscale images, I can't get several nucleus counter modes to work.

k-means clustering gives an error of:
Unrecognized command: "k-means Clustering"

Mixture modeling gives the error:
Unrecognized command: "Mixture Modeling threshold"

Is there some definition of these commands missing in the code?

Verify licensing and authorship of plugins

We need to double check the licensing and authorship of all these plugins. I'm not sure whether the provenance is actually known in every case. Ideally our README would list, for each plugin, who originally wrote it.

Delta F Down is not implemented

The Delta F Down plugin does not actually do anything. It has an empty for loop.

Reported by Christine Labno.

Some MBF plugins are missing from the cookbook

The goal of the Fiji Cookbook was to migrate the functionality of the MBF ImageJ distribution. However, some plugins are definitely missing: e.g., the RGB_Montage plugin. There are probably others—we should verify which and migrate them all to the Cookbook as appropriate.

Plugin or class not found: "CLI.Refresh_Macros"

I apologize if this is a dumb user error, but I installed the cookbook to test fly F div F0, but I get the error in the title when I try to execute it on an open image. The other t functions in the cookbook appear to work correctly. I am running on Mac OS 10.14.6 with ImageJ version 2.0.0-rc-69/1.52p.

Z stack depth coding

Hello everybody and @ctrueden,

It is not really an issue.
I've extended Z-stack color-coding function (Z_Code_Stack.java) from this project to:

• use multiple LUTs (not only "Spectrum"), plus one can invert colorcoding,
• also it works now with time series and can output either to RGB or composite stack.

I was wondering:

1. Can you add me to contributors, so I can update the code?
2. Can I use this re-written code for my own plugin? I guess this is a formality since it is under GPL3, so will be my plugin. I just don't need all other Cookbook functionality, so I decided to make a separate one (under slightly different name, etc).

Thanks in advance for your help/time.

Cheers,
Eugene

Organize Cookbook sources as a Maven project

The first version of the Fiji Cookbook has been uploaded to the Cookbook update site. The plugins are currently packed into a single cookbook_.jar file, without source code.

Next step is to grab the sources out of the MBF ImageJ distribution, add them to src/main/java here and turn the cookbook_ into a genuine Maven project. That way, we can hack on the Cookbook as needed to fix bugs, add features, etc.

Gotchas:

• Cell_Counter.java needed a couple of trivial tweaks in order to compile with the latest ImageJ.
• Beware: some plugins (e.g., Nucleus_Counter) have multiple versions of the source code. And in the case of Nucleus_Counter it gets worse: neither of the source versions match the compiled binary. So some sleuthing will be necessary to decide exactly what to ship, and what to add to Git.
• We need to double check the licensing and authorship of all these plugins. I'm not sure whether the provenance is actually known in every case.

Once this issue is resolved, we should update the Source and Credits sections of the front Cookbook page to reflect that.

Delta F Up does not differentiate between dimensions

The Delta F Up plugin loops over all image slices, and does not differentiate between Z, T and C positions. It should do so if it truly intends to provide a time differential.

Reported by Christine Labno.