Wiki

Clone wiki

Nuclear_Morphology / Frequently Asked Questions

Question Answer
How do I cite the program? See here
Why does the program produce an error message on launch saying "ClassLoadException on major.minor version"? The Java version is too low. The program needs at least Java 8. Update your system to Java 8 (or download ImageJ bundled with Java 8).
How can I save my preferred UI settings? Some options can be saved in a configuration file. See the config options for the available settings.
I loaded a dataset and got a message saying 'Corruption in dataset...'. There was a bug in earlier version which can affect segmentation in child datasets. The easiest solution is to redetect the nuclei (i.e. a new analysis), then import the .cell file containing the descriptions of the child datasets. The .cell file has been saved automatically to the current dataset folder. Follow step 2 onwards here.
How do I map FISH data to pre-FISH nuclei? See the guide here
What values are calculated for nuclei? See the list here
Microns and pixels have the same value. How do I get microns to show properly? Right click a dataset in the populations panel. Choose 'Set scale'. Enter the pixels per micron for your images. Click OK. The charts will be updated.
I want to download an old version, but it's not in the downloads page. The minor version number (z in x.y.z) only fixes bugs. Other behaviour should be the same. If you really want an exact older version, get in touch and I'll give you the files.
I have another question - how do I get in touch? You can find my contact details on my university webpage

Updated