Save Progress in Segmentation Editor?

Good Evening!

I’m wondering if anyone has tried to save and reload selections they have isolated in Segmentation Editor. Ideally, I’ld like to segment an image and save that selection so that I can analyze the data immediately in 3D ROI (this I can do). But I’d also come back reload the selection with the original image and analyze it again if neccessary. I can save the labels as a tiff file, but that is separate from the original image- I can’t seem to get them to merge again.

I found an old discussion in Nabble that mentioned using Amira plug-ins to save your selection and reload them at a later time. It mentioned that Segmentation Editor should automatically recognize the labels, but I end up getting an error (Internal: Unexpected end of ZLIB input stream) and the labels never overlap with the image of my brain.

Any suggestions would be greatly appreciated!!


Which Segmentation editor do you mean?

You can save selections if you transfer them to the ROI manager and save them to apply the ROI’s e.g. on the original image, see:

Hi @Bio7,

Thanks for responding!

I am using the Segmentation Editor developed by Johannes Schindelin, Francois Kusztos, Benjamin Schmid. Here is a link:

However, I am doing this in 3D though so the 3D is selected and I can’t use the regular ROI manager. It would be great if there was a way to save my progress and then reload it at a different time, but I can’t find that option.

Do you have any insight?

I would directly ask the maintainer of the plugin @bene.schmid since I never used this plugin.

Thanks @Bio7! I emailed @bene.schmid the other day so I will see if he has any insight and update the forum if a solution is found.

Thanks again!

Problem solved!

In order to save segmenting progress in Fiji, you should select:

File-> Save As-> AmiraMesh… and make sure to select the “labels” file.

To reload your segmented file, you should load your target file. Then select:
File-> Import-> Amira … and make sure to select your amira file.
Click on your target file (not the Amira file) and then load Segmentation Editor.

Your labels will automatically update on your target file.

If you are using Fiji and not ImageJ, you do not need to and should not download the “AmiraMesh…jar” and the “jzlib-1.0.7.jar” files to your plugin folder. The presence of the additional plugins interfere with Segmentation Editor’s ability to recognize your labeled Amira file.

Thanks @bene.schmid!!