- Our image-processing tools are compiled as the binary softwares on our image processing platform: VCAT5
- The binaries are for use on Windows (64bit version of Windows 7, 8.1, 10).
- Download the zip file (VCAT5porefree.zip). After unzip, double click VCAT5porefree.exe to run.
- The zip file includes the follwing files.
- Binary (VCAT5porefree.exe)
- Plugin folder (including binary files)
- Sample images (test01.tif, test02.tif, Masktest01.tif, Masktest02.tif)
Run
Extract all files in the archive, and open VCAT5porefree.exe.
Menu
- File
- Load
load TIFF images.
- Save
save active image to TIFF files.
- Exit
exit exe.
- View
- View Center
reset views to the initial position.
- Set BG Color
set background color.
- Set Window Level
open a dialog to set window level.
- Process
- KmeanAutoK
apply k-means clustering with automatic decision of K.
- PointsDetect
apply bright points detection based on geometric feature.
- Help
Section view
- Vertical scroll bar or mouse wheel
move the viewing section.
- Horizontal scroll bar or Space / Backspace key
when loading the 4D images, change the viewing image to previous/next time step.
- Left drag
move the image position in the window.
- Ctrl + mouse wheel
zoom in/out.
Sample execution
- KmeanAutoK
- File > load [test01.tif].
- Process > KmeanAutoK
- Set parameters in the dialog > MaskFile > set [Masktest01.tif]
- class-min : num of smallest clusters (default=2)
- class-max : num of largest clusters (default=10)
In the default case, kmeans is performed with various k (from 2 to 10).
- normalization: apply normalization to the exracted image features (=1), or not(=0).
- windowsize: local windows size for extracting image features (radius).
- MaskFile: set mask image or '0'(not in use). When using the mask image, non-zero pixels are subject to Kmeans.
- Run
- Save
- Save current displayed image.
- The two types of images are stored in the current directory ([input]_AllClusters_AnsK.tif, [input]_TargetCluster_AnsK.tif).
- AnsK means the selected number of clusters.
- [input]_AllClusters_AnsK.tif: The result image of kmeans using selected k. This image is same as the current displayed image.
- [input]_TargetCluster_AnsK.tif : The result image remaing only the target region. In this case, the target means the pore-fre island.
- PointsDetect
- File > load [test02.tif].
- Process > PointsDetect
- Set parameters in the dialog > MaskCellFile > set [Masktest02.tif]
- MaskCellFile: set mask image or '0'(not in use). When using the mask image, non-zero pixels are subject to PointsDetect.
- Run
- Save
- Save current displayed image.
- The two types of images are stored in the current directory ([input]_binarization.tif, [input]_Points.tif).
- [input]_binarization.tif: the result image of binarization.
- [input]_Points.tif: the reporesentative positions are showed in the binarized image.
S.Takemoto, satoko-t[_at_]riken.jp
Last Update: 25 September 2017