Hi there I have a 16bit raw image stack of a segmentation ‘so it doesn’t have a crazy amount of colors in the image itself’. Is there a way in slicer to generate a segment for every existing color in the image using the segment editor? Hopefully slicer can handle a fairly large number of segments. …

Thank you so much for the quick reply, I won’t be able to try this until tomorrow. Just one question in regards to your answer, will I be able to re-sample while using the method in the other thread

Yes, you can crop and resample labelmap volumes the same way as scalar volumes, just make sure to use nearest neighbor interpolator if you want to preserve original voxel values at the boundaries.

After trying this method with about 1/8th of the dataset, which is a 700mb nrrd file. It did work but took a very long time to compute and with the labels it uses about 98percent of my 16gigs of ram. I will try some other software packages but I feel like they will also be too resource heavy

Currently, you can can probably edit up to about 30-50 segments at a time and move out other segments to another segmentation or labelmap. We are improving the segment editor to better support some neurosegmentation workflows which may involve a few hundred segments. What kind of data do you work w…

It is a micro-ct of a mammal and has I estimate it will have north of 200 segments if I was to load in the full dataset. Unfortunately I am interested in preserving as much detail as possible so reducing the quality isn’t really an option. Looking forward to future updates to the segment editor.

Sorry I am not sure how to check that. However today I did try to do the same with the 1/8th data set using both Itk-snap and Mimics. I wasn’t able to find where to import a labelmap for mimics ‘it probably doesn’t have this functionality’, but with itk-snap I just clicked open segmentation and open…

[image] the3dslicerdude: Sorry I am not sure how to check that If you keep your mouse cursor above the CT in the Data module, the tooltip will contain the image size. You can also check these (and more) details in the Volumes module. [image] the3dslicerdude: itk-snap I just clicked open …

Yes, segment editor is much more capable than ITK-snap but currently it uses an separate labelmap for each segment, which may require significantly more memory, especially when you have many segments. We’ll make editing of hundreds of segments more efficient within a couple of months (allow sharing…

Sorry to revive this much later, but I hope someone can help: I am having a stack of png-images with 5 different colors in them. I’d like to segment this by color, mainly select the white background and remove it to 3D render the rest. But when I try to load the image stack as a label map, I just g…

New segment for every colour

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lassoan (Andras Lasso) July 18, 2019, 12:51pm 2

It sounds like you have a labelmap volume (you have discrete values in the volume, each value corresponds to a certain structure). You can follow these instructions to load this image and import to segmentation:

Topic		Replies	Views
.nrrd files segments to label map volume Support	2	283	September 24, 2021
Export Segmentation as Labeled LabelMap Support	17	3888	May 12, 2023
Importing labeled image to segment directly Support segmentation , labelmap	2	1852	March 9, 2020
Display a segmented data in Slicer 3D view Support	2	1876	August 8, 2019
Loading multiple labelmaps (label masks) Support segmentation	2	1987	August 16, 2019

New segment for every colour

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