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MPIBR-juneks edited this page Jul 1, 2016
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matVis is a Matlab GUI for displaying data sets of arbitrary dimension using 2D images and 1D profiles. Key features of matVis include
- Easy data input: load variables from the workspace or various image file formats including Zeiss lsm-files and .mat-files
- Easy navigation through data sets of arbitrary dimension
- Easy to learn user interface with tooltips for each control item
- Visualize multiple data sets of identical dimensions in parallel
- Histogram-guided contrast adjustment including gamma correction and algorithmic thresholding
- Large variety of colormaps
- Image and plot filter
- Image projections including image tiling
- RGB display including color-coded max- and mean-projections ('RGB stretch')
- Extensive region of interest manager
- Video generator, which can combine the content of mutiple windows into
a single customizable movie - Specify scales, names and units for the data dimensions
- Use of alpha data including contrast and gamma adjustments
- 2D histogram for image data / alpha data with histogram guided 2D contrast adjustment
- Figure and function handles can be accessed from 'outside', making matVis easy to integrate with other GUIs or Matlab functions
- Save configuration (settings, window positions, ...) for future use
- Use 'startPar' argument to selectively overwrite configuration paramaters (see below for list of start parameters)
- Check for updates from within the main GUI
-none- Select image file(s) (including matrices
saved as .mat-file, multi-image tif, Zeiss
lsm-files, RGB files, animated gif and most
other image formats) via uigetfile. Files
can be combined into a single matrix or
opened "in parallel".
data1, data2, ... Data sets of arbitrary but identical dimension
'pathname\filename.ext' Path- + filename of desired file (works only for
one file)
'dimScale' Scale for dimensions, i.e. values of bounds
of 'pixel-locations' (like the x and y paramteres in
imagesc(x,y,d))
'dimNames' Cell array containing dimension names, e.g.
names = {'x';'y';'z';'time';'lambda'};
Make sure that size(names,1) == ndims(data{1}).
If omitted, dimensions will be named
Dim1 , Dim2, Dim3, ...
'dimUnits' Units of dimensions (simply for display purposes)
'matNames' Names of matrices displayed in Figure Name.
Needs to be specified as a cell array of
strings, even if only one matrix is
specified.
Default is the name of the variable in the matlab workspace, but if an
expression is used (such as d(:,:,1)), it will be empty leaving
matVis to display an empty string.
'alphaMap' Alphamap, has to be of same size as data
matrix. Useful for masking images. Background color will
be set to black.
'startPar' List of configuration settings. These
settings 'override' the custom settings saved in a customConfig
file (if available). The list should be a cell array with the
common {'propertyName1'; 'propertyValue1'; 'propertyName2';
'propertyValue2';...} structure. The following properies can be
set:
xySel x- and y-dim for image display
zoomVal Matrix indicating zoom setting
plotDim Dimensions along which plots will be displayed
plotMean Number indicating status of plot-average-mode: 0: 1x1, 1: 3x3, 2: 5x5, 3: [1x1,3x3,5x5], 4: zoom area, 5: RGB
currPos Vector indicating starting position
cmMinMax Matrix of size 2 x number of data sets for colormap limits
cmap Number of colormap from list of available colormaps: {'Gray';'Gray (Range)'; 'Jet'; 'HSV'; 'Hot'; 'Cool';
'Red 1';'Red 2';'Green 1';'Green 2';'Blue 1';'Blue 2'; 'Rainbow1';'Rainbow2';'Rainbow3';'Rainbow4';
'Blue-Gray-Yellow (0 centered)';'Magenta-Gray-Green (0 centered)'}
aspRatio Two element vector
rgbDim Number of RGB dimensions
projDim Number of projection dimensions
projMethod Number or string: {'None';'Max';'Min';'Mean';'Std';'Var'; 'Tile'}
windowVisibility Binary vector indicating visibility of [imageWin zoomWin plotWin]
windowPositions Structure s containing the fields s.gui, s.imageWin, s.zoomWin and s.plotWin. In case there is one data set,
the values of the fields are four element vectors [x0, y0, width, height], in case there are nMat data sets,
the values are matrices of size nMat x 4.
WARNING: gui Position includs TooltipDisplay!!!
Structure containing the following fields:
- figHandles: figure handles to all figures, including main GUI
- fctHandles: function handles of functions useful for 'data
exchange' or 'external' update of matVis settings
- settings: structure containing information about current settings
(currently zoom and zoomXY)
- dataName: cell array containing names of the loaded data
Left click and drag Draw zoom region
Right click Unzoom
Left click and drag in Zoom Rectangle Move zoom region (pan)
Middle click or Shift + left click Move Position Lines
Double click Copy content of current figure
to clipboard (either as bitmap or vector graphics).
Works only for Windows OS.
Right click in main gui Bring all visibile windows on
top of the screen
Scroll Wheel (Matlab 2007a or later) Zoom in and out (for zoom and
image windows)
Instead of using sliders or text boxes to change the current position values,
you can use the number keys on the keyboard instead. Press '1' to increase
the current value of Dim1 by one, press 'control'+'1' to decrease its
value by one,... This is however only possible if the main gui is the
current figure (i.e. the selected window) and none of its controls is active
(click in some empty space within the gui if it doesn't work as you
expect).
Works also only for the first nine dimensions :(
RGB display can be toggled with the RGB button. You can use RGB display
for each dimension that is not used as either 'x' or 'y' dimension. As
you press the RGB button you switch between all possible dimensions.
The current image is displayed as the green channel, the preceding as
red and the succeeding as the blue channel. If there are only two
values in the selected dimension the blue channel will be left empty.
If you select the 'Stretch RGB' option, a colormap along the complete
dimension will be created such that red corresponds to high intensities
in the initial part, green to high intensities in the intermediate part,
and blue to high intensities in the late part of the selected
dimension. Changing the position of the slider of this dimension does
not have any effect.
Note that some functions (e.g. histogram, export data) are so far only supported for the first data set! Using them while multiple data sets are loaded might lead to errors!
See end of this file for a list of known bugs and planned feature implementations. See http://www.colors-and-contrasts.com/Documents/matVisGuide.pdf for a complete manual (can also be accessed from the main Gui of matVis). Manual is not completely up to date. Please contact me if you have questions / bug reports / feature requests!
Copyright 2016, Stephan Junek (stephan.junek@brain.mpg.de)