Hi all (specially @lassoan and @cpinter ), I am working with a 2D segmentation. After saving it, I use Python to process the NRRD files. The size of my master volume node is 28320 x 15232, it’s a scanned histological slice with 2 µm resolution. We hace 24 segments extending pretty much all around th…

This seems to have been addressed recently: New feature: Shared labelmap segmentations .

[image] Fernando: 28320 x 15232, it’s a scanned histological slice with 2 µm resolution. We hace 24 segments extending pretty much all around the slice, so the size of my NRRD array is 26013 x 13644 x 24, which takes about 8 GB of RAM and I can’t use my computer anymore when I try to open the fi…

[image] lassoan: It could be possible to define groups of segments that are not allowed to overlap and store them in a labelmap, but there are many higher-priority tasks, so probably this would not be available for at least 1-2 years. If you’re reading this in 2019, and in case this can help,…

[image] Fernando: What if I want to show all of them again after that operation In Segmentations module: select all segments in the segment list, right-click, “Show only selected segments”. [image] Fernando: I can’t say I know what virtual memory is, sorry. On Linux, virtual memory is…

For histology, the usual approach is to resample and tile at multiple zoom levels. Then you can show the whole slide overview and lazy-load only a small subset of the high resolution tiles as the user zooms in and moves around (either from separate tile files, or by mmap’ing the whole file and pulli…

At some point I think Brad Lowekamp implemented a simple CLI module that took a ROI and a filename as an input and it returned the requested part of the image as an output. It made really easy to retrieve a certain portion of a large image. I think it used the MetaIO format, which has a nice reader …

[image] ihnorton: Kitware has (or had) one too https://digitalslidearchive.github.io/HistomicsTK/

@lassoan [image] lassoan: On Linux, virtual memory is referred to as “swap” ➜ ~ free total used free shared buff/cache available Mem: 16353852 10332076 1450964 475936 4570812 5110556 Swap: 16698364 440 16697924 …

It send that you only configured to have 16GB of virtual memory. I usually set virtual memory size 5-10x the size of the data set I’m processing.

I added some swap but still can’t get Slicer to open the segmentation: ➜ ~ free -h total used free shared buff/cache available Mem: 15G 6,2G 6,5G 127M 2,9G 8,9G Swap: 65G 0B 65G [image…

Resampling does not happen immediately when you import the labelmap (as resampling may be a lossy operation or it may take a long time to compute), but only performed when it is needed (e.g., when the segment is modified). Maybe if you use Copy operator of Logical operators effect then the result is…

Segmentations can get big!

Support

Topic		Replies	Views
Can't save the scene and the segmentations - allocation ERROR, results undefined Support	18	883	July 29, 2019
Loading seg.nrrd files very slow or failing Support segmentation	7	438	July 26, 2022
Bad performance when segmenting 11GB micro-CT Support segmentation	12	319	September 16, 2024
Segmenting out of border of main volume Support	11	822	September 4, 2021
New feature: Shared labelmap segmentations Support feature , segmentation	1	911	October 23, 2019

Segmentations can get big!

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