Slicer

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

Description

Simple interface for exploring 3D images by visualizing planar slices. It is not a 3D renderer, but allows to get a quick overview of the image.

Among the interface features:
- navigation within image,
- zoom management,
- edition of grayscale range (from datataype, from image, manual)
- 3D image flip or 90-degrees rotation,
- management of image resolution
- import of metaimage, analyze or dicom images
- display of 3 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

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

• Required Products: Image Processing Toolbox
• MATLAB release: MATLAB 7.9 (2009b)

[J Rey]

Excellent, thank you very much.

[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.

[sdf]

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

[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.

[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]

@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 ?

[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]

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