Hi Malte, I’m not sure of I understood you exactly but regarding the stack of 2d images, we do not support this kind of formats as they usually throw away important information like slice thickness or even real world coordinates. While it may be sufficient for some workflows to work purely on an abstract pixel-level, we experienced that people using these kinds of simple file formats get in trouble sooner or later as important meta-information is sometimes lost forever or impossible to recreate.
Established 3d image file formats in medical imaging that are easy to read/write (in contrast to DICOM) and still preserve most of this information important for scientific processing are NRRD or NIFTI for example. Regarding single vs. multiple segmentations we have two sets of segmentation plugins in MITK: Single-label segmentation (binary masks) and multi-label segmentation (including multiple Photoshop-like layers if overlapping segmentations is a requirement). The segmentations created by the latter plugins can be saved into single 3d image files instead of multiple 3d image files per segmentation. From: Malte Wallmeier [mailto:malte...@kth.se] Sent: Wednesday, October 30, 2019 11:16 AM To: mitk-users@lists.sourceforge.net Subject: [mitk-users] Export segmentation Hej MITK-pros, I am manually segmenting fibers in synchrotron tomography images of a natural fiber material. Is there a way to export the whole segmentation image (not just single segmented fibers) as a 3D-tiff of stack of tiffs? Best regards Malte Wallmeier [KTH_Logotyp_RGB_2013 small] KTH Royal Institute of Technology School of Engineering Sciences Department of Solid Mechanics SE-100 44 Stockholm, Sweden E-mail: malte...@kth.se<mailto:malte...@kth.se> www.kth.se<http://www.kth.se>
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