VoTracer I/O

VoTracer I/O Basic Manip. Visualization Segmentation Refinement Top

This page explains functions for inporting and exporting images．

Load image
I-1) File > Load Volume Image (tif,sph,vcat)
I-2) File > Load Slice Images (dcm,bmp,raw)
I-3) File > Load 2nd channel (tif,sph)
I-4) File > Load 2nd channel (slices)(dcm,bmp)
I-5) File > Load 3rd channel (tif,sph)
I-6) File > Load 3rd channel (slices)(dcm,bmp)

Save and load mask data (application specific format)
M-1) File > Load Mask Data (vtmask3,vtmask2,vtmask)
M-2) File > Save Mask Data (vtmask3)

Export Image
File > Export Volume >
Ev-1) Export as 64bit multipage Tif (no tone mapping)
Ev-2) Export as 8bit multipage Tif (normalized by window level)
Ev-3) Export as Bmp slices (normalized by window level)

Export mask data
Emr-1) Export Mask as 8bit Tif (.tif)
Emr-2) Export one region as Obj (.obj)
Emr-3) Export one region as Stl (.stl)
Ec-1) File > Export Volume mask as Vcat (.vcat)

Load image

I-1) Menu > File > Load Volume Image (.tif, .sph, .vcat)

This item is for loading volumetric (3D) images (*.tif, *.sph, *.vcat).
*.vcat is a data format use in VCat 1.5 that contains image and mask.
If a colored image is loaded, dialog that asks loading format will appear.

I-2) Menu > File > Load Slice Images (.dcm, .bmp)

This item is for loading multiple slice images (.dcm, .bmp)
To load *.dcm file，installation of xmedcon is required.
If a colored image is loaded, dialog that asks loading format will appear.

I-3) Menu > File > Load 2nd channel (.tif, .sph)
I-4) Menu > File > Load 2nd channel (slices)(.dcm, .bmp)

This item is for loading 2nd channel image (gray scale).
This item is available after loading 1st channel image (gray scale).
2nd channel image should have the same resolution to the 1st channel image.

I-5) Menu > File > Load 3rd channel (.tif, .sph)
I-6) Menu > File > Load 3rd channel (slices)(.dcm, .bmp)

This item is for loading 3rd channel image (gray scale).
This item is available after loading 2nd channel image (gray scale).
3rd channel image should have the same resolutions to the 1st and 2nd channel images.

Save and load mask data

>M-1) Menu > File > Load Mask Data (.vtmask2)

Save the current mask data as .vtmask2 format

>M-2) Menu > File > Save Mask Data (.vtmask2)

Load a mask data (.vtmask2). Mask data should be same resolution to the loaded volume image.

Export Image

Ev-1) File > Export Volume > Export as 64bit multipage Tif (no tone mapping)

Export the input volumetric image as multi-page 64 bit (double) tif, without tone mapping.

Ev-2) File > Export Volume > Export as 8bit multipage Tif (normalized by window level)

Export the input volumetric image as multi-page 8 bit tif (.tif).
Voxel values are normalized in to [0, 255] by using min/max window level.

Ev-3) File > Export Volume > Export as Bmp slices (normalized by window level)

Export the input volumetric image as bitmap slices (.bmp).
Voxel values are normalized in to [0, 255] by using min/max window level.

マスクエクスポート

Emr-1) File > Export Mask or Region > Export Mask as 8bit tif (.tif)

Export mask data as 8bit multi-page-tif.
Voxel value [0,255] corresponds to the IDs of ROIs.

Emr-2) File > Export Mask or Region > Export one region as Obj (.obj)

Export a ROI as triangle mesh model (.obj)
The system provides dialogs for ID selection and marching cubes parameter selection.

Emr-3) File > Export Mask or Region > Export one region as Stl (.stl)

Export a ROI as triangle mesh model (.stl)
The system provides dialogs for ID selection and marching cubes parameter selection.

Ec-1) File > Export as VCAT file (.vcat)

Export volumetric image and mask as Vcat format
See this page for detail of VCAT

z stack direction

2015/3/31以降は以下の実装です。

VoTracerは、bmp/dcm/(multipage)tifなどの入力画像を受け取ります。
これらは二次元のスライス画像群で、原点は左上（windowsの仕様）です。

画像データやマスクデータの読み込み後、VoTracerは以下のダイアログを表示します．
画像をスタックする方向を指定してください。

ダイアログ中の図の通り、三次元空間の原点は左上手前になります。
（ここは2015/3/31より前のVoTracerとは異なります。）
※読み込み時にDescending orderを選択した場合、その後画像やマスクをexportすると，z軸方向に反転したものが出力されます
※画像とマスクは同じスタック方向を指定する必要があります．

2015/3/31より前の実装は、下図のように三次元空間の原点を左下奥にとり、スライスを置くから手前にスタックしました。
2015/3/31より前の実装では、スタック方向の指定は出来ませんでした。

※また、三次元空間の原点を左下に置くために、内部的には画像をy軸方向に反転したデータを持っているなど、コードもあまり綺麗ではありませんでした。今後は、上記の新しい実装をベースに開発を進めます。

Required RAM/VRAM on your computer

VoTracer requires large memory (RAM) on your computer.
For gray scale image, it requires about V * 12 Byte (V is the number of voxels).
e.g.) it requires 1.6GByte RAM for 512x512x512 volume image.

For color image, it requires about V * 22 Byte.
e.g.) it requires 2.9GByte RAM for 512x512x512 volume image.

VoTracer requires large memory (VRAM) on your graphics card.
For gray scale image, it requires V * 4 Byte (V is the number of voxels).
For gray scale image, it requires V * 6 Byte (V is the number of voxels).

Even I do my best to save the RAM, it requires still large…