3D Slicer

Slicer for exploring 3D images (grayscale, color or vectorial) through planar or 3D slices.

Description

Simple interface for exploring 3D images by visualizing planar slices. The interface also allows to display 3 orthogonal slices, either in 3D or in three subplots.

Among the interface features:
- navigation within image,
- zoom management,
- edition of grayscale range (from datataype, from image, manual)
- interactively change display range, color map, spatial resolution...
- 3D image flip or 90-degrees rotation,
- import of metaimage, analyze or dicom images
- interactive 3D orthogonal slices, planar or 3D
- management of several look-up tables

It supports 3D grayscale, binary, RGB, or vector images (in this case, the vector norm is used for display).

The package includes functions to read/write image stacks stored as tif slices or bundle, as well as basic support for reading and writing images in metaimage format (mhd).

Examples of use:
 Slicer(img); % display the 3D or 4D imge
 Slicer('fileName.tif'); % read the 3D image from file
 Slicer('img000.tif'); % read a series of images
 Slicer % opens a dialog to choose the file
 Slice(img, 'DisplayRange', [0 80], 'Spacing', [1 1 2.5], 'Origin', [0 0 0], 'unitName', 'µm'); % Specify some options

Type "help slicer" at matlab prompt, or "help imStacks" to have an overview of all functions within the package.

To install, simply unzip, and add the directory "imStacks" to the path. The new version of the Slicer (from July 2012) uses the GUILayout toolbox by Ben Tordoff (FEx #27758). Version 1.10 is included in the archive for convenience.

Acknowledgements

Myslicer Make Mouse Interactive Slices Of A 3 D Volume and Gui Layout Toolbox inspired this file.

• Required Products: Image Processing Toolbox
• MATLAB release: MATLAB 8.0 (R2012b)

[David Legland]

Hi Niru C,
This contribution is devoted to the visualisation of 3D images. For your problem, I would suggest trying my other contributions geom3d (#24484) and geom2d (#7844), in particular functions intersectPlaneMesh, and polygonLength.

[Niru C]

Hello David

I have this 3D point-cloud which I made into a triangulation mesh (~4500 points) using the ball-pivot algorithm. I want to find the perimeter of an outline formed from intersection of this 3D mesh and a plane parallel to XY plane say at different Z values. Can I do this in this program ? What will be your suggestion?

Thank you

[Sean de Wolski]

Hi David,

I had to grab the "Patch" folder from the GUI Layout Toolbox in order to avoid run time errors.

%Sean

[Gianni Schena]

This function offers the same capability available with expensive commercial software for CT / MR explotation.
It would be desirable to have an option to generate the histogramm of the voxels-luminosity (excluding the background voxels ) e.g. like : hist(Volume(good_voxels),nbins).
The valley of the histrogram can used for region-based volume segmentation.

[Gianni Schena]

 

[David Legland]

Hi Martijn,
your suggestion is good ! I have just submitted an updated version that fixes it. I'll also try to add support for data stored in header file in a future version.

Regards,
David

[Martijn Steenwijk]

Hi David,

Great work! A small suggestion regarding the metaImageInfo function. Currently, if a mhd file contains the tag ElementSize, but not the tag ElementSpacing, ElementSpacing will be set by default as [1 1 1].

This while the specification states (http://www.itk.org/Wiki/MetaIO/Documentation):
If ElementSpacing is not specified, it is assumed to be equal to ElementSize. If neither is specified, both are assumed to be 1.

Would it be an idea to follow this ITK convention?

Best,
Martijn

[David Legland]

@OPS:
I think the problem depends on the image you tried to visualize.

Input should be either a M*N*P 3D grayscale image, or a M*N*3*P 3D color image.

hope this helps ?

[ops OPS]

not work for me
??? Index exceeds matrix dimensions.

Error in ==> slicer>computeDisplayData at 415
data = img(:, :, zslice);

Error in ==> slicer>setSlice at 656
cdata = computeDisplayData(handles);

Error in ==> slicer>slicer_OpeningFcn at 216
setSlice(handles);

Error in ==> gui_mainfcn at 221
feval(gui_State.gui_OpeningFcn, gui_hFigure, [],
guidata(gui_hFigure), varargin{:});

Error in ==> slicer at 124
gui_mainfcn(gui_State, varargin{:});

[David Legland]

@sdf: It is actually possible to load dicom images (files->import->dicom). Note that the gui does not support all dicom features. I have submitted an updated version, that should be more intuitive.
If you still have some bugs, please email me.

[sdf]

do not open .dcm image....error of
Index exceeds matrix dimensions.

[sdf]

??? Attempt to reference field of non-structure array.

Error in ==> slicer>itemOpen_Callback at 980
[filename, pathname] = uigetfile( ...

Error in ==> gui_mainfcn at 96
feval(varargin{:});

Error in ==> slicer at 113
gui_mainfcn(gui_State, varargin{:});

Error in ==>
@(hObject,eventdata)slicer('itemOpen_Callback',hObject,eventdata,guidata(hObject))

??? Error while evaluating uimenu Callback

plyz tell me my mistake..and i have also added path to matlab.

[J Rey]

Excellent, thank you very much.