Michael Doube

Move user documentation links from imagej.net/BoneJ to https://imagej.net/plugins/bonej

10

**Describe the bug** ImageJ Wiki docs have been / are being moved from imagej.net to https://imagej.github.io/ Links need to be updated. - [ ] bonej.org `index.html` - [ ] bonej.org...

Add 3-3-2 surface colour regime so that 3D surfaces match 2D particle default LUT

1

**Describe the bug** Particle colours in 3D Viewer don't match colours in the particle image **To Reproduce** Steps to reproduce the behavior: Run particle analyser with Particle Image and Show...

**Describe the bug** Test fails with `An error occurred while opening the image` instead of `Image format is not recognized` **Expected behavior** Test passes **Environment** commit 4bc1bd5dc scijava 29.2.1 **Additional...

EF default output is way too verbose.

2

**Describe the bug** There is too much information in the EF output for the default case, which should be just the EF image, and in the results table EF min,...

Ellipsoid Factor throws a Null Pointer Exception when other images are open

2

``` (Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 645MB of 48839MB (1%) java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309) at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163) at ij.IJ.runPlugIn(IJ.java) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at...

**Describe the bug** Ellipsoid Factor can calculate an average over several runs to help smooth the result. The current implementation is a bit inefficient on memory because several image copies...

**Describe the bug** It is hard to guess what settings will result in a reasonable estimate of anisotropy for a given image. BoneJ1 included the option by default to keep...

Surface Area complains that axis calibrations are different when they are the same

3

**Describe the bug** Surface Area always complains that axis calibration is different even when it is the same, then returns an uncalibrated surface area. **To Reproduce** Steps to reproduce the...

**Describe the bug** IJ2 Ops currently mesh over an uncalibrated pixel grid, but measurements are needed in real units. Calibration improvements to the meshing ops are coming, according to these...

I had a good reason not to do it that way. IIRC sorting columns didn't quite work, i.e. results didn't "follow" their channels/frames. However, that is no longer the case....