Chopped images...
This section allows to chop a large dataset to smaller pieces and restore them back. This feature may be useful when needed to parallel segmentation of the large dataset to several workstations.
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Contents
出口. ..
The export command chops the large dataset into smaller pieces.
- Number of tiles in X/Y/Z, define number of resulting datasets. For example, whennumber of tiles in X: 2, in Y: 1 and in Z: 1the original dataset will be chopped in two smaller datasets. The first dataset will have dimensions [1:width/2] and the second [width/2:width], wherewidthis the width of the original dataset
- Chop model, when model is present it can also be chopped into corresponding blocks, if this checkbox is selected
- Chop mask, when the Mask layer is present it can also be chopped into corresponding blocks, if this checkbox is selected
- Output directoryuse this button or the editbox to define directory where the chopped datasets should be saved
- Filename template, defines a template for saving the chopped datasets. During the saving MIB will add "_Znn_Xnn_Ynn" tag to each block, wherennis the index of the block.
- Output format for images, datasets can be saved in Amira Mesh, NRRD, 3D-TIF formats, or HDF5 with XML header formats.
- Output format for models, models can also be stored in several formats: Matlab, AmiraMesh, NRRD, TIF or HDF5. When the models are saved a "Labels_" prefix is added to the beginning of the filename.
面具在Matlab格式保存Mask[FN].mask_ template, where [FN] is a filename of the corresponding image dataset.
Import...
The import command restores previously chopped or cropped datasets.
There are two modes available:
- Generate new stack, generates a new stack (for images), or imports models or masks for the opened datasets. When using this mode it is important to have proper filenames. The images should have the "_Znn_Xnn_Ynn" tag at the end of the filename; the models should have the "Labels_" prefix (see theExportsection for details). This is default mode for combining files that were chopped using the Menu->File->Chopped images...->Export... command
- Fuse into existing, uses the BoundingBox information that is normally stored in the ImageDescription field to fuse the selected datasets into the opened dataset. This mode can be used to import previously cropped datasets and models.
To proceed please choose the mode and types of the files to combine. After that press theSelect filesbutton to choose the files. The filenames for the models and masks are automatically generated from the filenames of the selected images:
- Filename of the selected image:Huh7_CmVTag1_R2_Pos5_crop_chop_Z01-X01-Y01.am
- Generated filename of the model:Labels_Huh7_CmVTag1_R2_Pos5_crop_chop_Z01-X01-Y01.mat
- Generated filename of the mask:Mask_Huh7_CmVTag1_R2_Pos5_crop_chop_Z01-X01-Y01.mask
Important!If theImagescheckbox is selected please select only files with images and do not select models nor mask files. The filenames for models and masks will be automatically generated. However, if models or masks are combined for the opened dataset (i.e.theImagescheckbox is unselected) the actual model or mask filenames have to be selected.
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