I have two time-lapse images of a membrane surface. Both images were supposed to show the same region. But while adjusting focus, captured field might have drifted a bit. I used two routes to visualize the amount of drift - MATLAB v 2021a and ImageJ. With MATLAB, first I tried superimposing two images using imshowpair. Original grayscale images are fix
and mov. imshowpair(mov,fix) yields imshowpair_comp. It clearly shows possible drift. Then I tried using imfuse function as follows:
RF = imref2d(size(fix));
RM = imref2d(size(mov));
RM.XWorldLimits = RF.XWorldLimits;
RM.YWorldLimits = RF.YWorldLimits;
comp = imfuse(fix,RF,mov,RM,'falsecolor','Scaling','joint','ColorChannels',[1 2 0]);
It gave the composite image imfuse_comp. Next, I carried out image registration and I got imregcorr_comp.
tForm = imregcorr(mov,fix,"similarity");
movTransform = imwarp(mov,tForm,"OutputView",RF);
imshowpair(movTransform,fix)
This image shows properly aligned composite image. I tried doing the same using ImageJ.
Open fix.tiff in ImageJ. Image->Colors->Channels Tool->Composite->Red.
Open mov.tiff in ImageJ. Image->Colors->Channels Tool->Composite->Green.
Image->Colors->Merge Channels
This gave the composite image imagej_comp. This composite image obtained from ImageJ clearly shows that there was no misalignment in the two images to begin with!
I am unable to figure out where I went wrong. Now I am really confused between two routes - and which route to believe in. Can someone please help me out?
Thanks!
Related
I have troubles extracting a tumor using a RT mask from a dicom image. Due to GDPR I am not allowed to share the dicom images even though they are anonymized. However I am allowed to share the images themself. I want to extract the drawn tumor from the CT images using the draw GTV stored as a RT structure using MATLAB.
Lets say that the file directory where my CT images are stored is called DicomCT and that the RT struct dicom file is called rtStruct.dcm.
I can read and visualize my CT images as follows:
V = dicomreadVolume(“DicomCT”);
V = squeeze(V);
volshow(V)
volume V - 3D CT image
I can load my rt structure using:
Info = dicominfo(“rtStruct.dcm”);
rtContours = dicomContours(Info);
I get the plot giving the different contours.
plotContour(rtContours)
Contours for the GTV of the CT image
I used this link for the information on how to create the mask such that I can apply it to the 3D CT image: https://nl.mathworks.com/help/images/create-and-display-3-d-mask-of-dicom-rt-contour-data.html#d124e5762
The dicom information tells mee the image should be 3mm slices, hence I took 3x3x3 for the referenceInfo.
referenceInfo = imref3d(size(V),3,3,3);
rtMask = createMask(rtContours, 1, referenceInfo)
When I plot my rtMask, I get a grey screen without any trace of the mask. I think that something is wrong with the way that I define the referenceInfo, but I have no idea how to fix it or what is wrong.
volshow(rtMask)
Volume plot of the RT mask
What would be the best way forward?
i was actually having some sort of similar problem to you a couple of days ago. I think you might have two possible problems (none of them your fault).
Your grey screen might be an error rendering that it's not showing because of how the actual volshow() script works. I found it does some things i don't understand with graphics memory and representing numeric type volumes vs logic volumes. I found this the hard way in my job PC where i only have intel HD graphics. Using
iptsetpref('VolumeViewerUseHardware',true)
for logical volumes worked fine for me. You an also test this by trying to replot the mask as double instead of logical by
rtMask = double(rtMask)
volshow(rtMask)
If it's not a rendering error caused by the interactions between your system and volshow() it might be an actual confusion and how the createMask and the actual reference info it needs (created by an actual bad explanation in the tutorial you just linked). Using pixel size info instead of actual axes limits can create partial visualization in segmentation or even missing it bc of scale. This nice person explained more elegantly in this post by using actual geometrical info of the dicom contours as limits.
https://es.mathworks.com/support/search.html/answers/1630195-how-to-convert-dicom-rt-structure-to-binary-mask.html?fq%5B%5D=asset_type_name:answer&fq%5B%5D=category:images/basic-import-and-export&page=1
basically use
plotContour(rtContours);
ax = gca;
referenceInfo = imref3d(size(V),ax.XLim,ax.YLim,ax.ZLim);
rtMask = createMask(rtContours, 1, referenceInfo)
In addition to your code and it might work.
I hope this could be of help to you.
This is a fairly entry-level question but I could not find the answer to it here on SO or on Mathworks help.
I want to add a color bar to an image I am loading and then save the image along with the created color bar.
The result I am looking for is like figure 1 on this page except that there is an image instead of the plot and the color bar shows the range of intensities in the image.
The page made me think that running
colorbar(<trarget matrix>);
Would do the trick but that throws an error when I try to apply it to an image.
So my question is, how do I make a color bar for my image and once made what would be a good way to concatenate the two for saving.
I am loading the image using the following snippet
IMGpath = 'barbaraSmall.png';
im = imread(IMGpath, 'png');
%
%colorbar(im); >>Throws an error
imshow(im);
imwrite(im, 'barabara_withMAP.png', 'png');
The syntax that you're using is colorbar(target). According to the documentation,
target is:
"Target for the colorbar, specified as an Axes object, a PolarAxes object, or a graphics object that has a ColorbarVisible property".
You're inputting an image matrix (im) as target which is none of the above mentioned objects. You can simply just enter:
colorbar;
or if you want to give an axes' handle then:
colorbar(gca);
You can save the result using saveas.
saveas(gca, 'barabara_withMAP.png')
I am currently recording on a single camera the images, one aside of the other one, of the same sample out of a microscope.
I have 2 issues with that, and I figured out that in post procesing with Matlab I could arrange these questions.
-First, the 2 images on the camera are supposed to have the same pixel size, or one is just a litle bigger than the other one, probably because of optical pathways. What is the adapted Matlab function or way to correlate the two images so they will have exactly the same pixel size in X and Y ?
Two images on same camera , one bigger or smaller compared to the other one
-Secondly, my sample is moving a litle during the recording ( while still staying in my field of view of course ). To make my analysis easier, it would be suitable that I could correct the images so the sample remain at the same place as in the first image, to perform calculations on it easier. What would be the adapted Matlab function or way to correct this movement in the image ?
Sample moving in the image on the camera
Sorry for the poor quality of my drawings !
Thank you very much for your advices and help.
First zero-pad the images to a sufficient degree, to get them both to double the size of the bigger one.
size_padding = max(size(fig1),size(fig2));
fig1_pad = padarray(fig1,size_padding-size(fig1),'post');
fig2_pad = padarray(fig2,size_padding-size(fig2),'post');
Assuming the sample is the only feature present in the images, the best way to proceed would be to use the xcorr2() function and find the lag corresponding to the maximum correlation, to get the space shift between the two images:
xc = xcorr2(fig1_pad,fig2_pad);
[max_cc, imax] = max(abs(xc(:)));
[ypeak, xpeak] = ind2sub(size(xc),imax(1));
corr_offset = [ (ypeak-size(fig2_pad,1)) (xpeak-size(fig2_pad,2)) ];
You then use circshift() to shift one of the images using the lag you obtained in the last step.
fig2_shift = circshift(fig2_pad,corr_offset);
You now have two images of the same size, where hopefully the sample is in the same position. If you want to remove the padding zeroes, crop the images to your liking with respect to the center using imcrop().
I'm making a GUI in MatLab that asks the user to upload a video file.
Next I want to play it in axes with a fixed window size . However, if the uploaded file is large, Matlab will expand the axes and take over most of my GUI. Is there a way to shrink the image to make it fit the axes?
Does anyone know how to solve this?
Usually Matlab axes are not supposed to change their position if the image is too big.
I can think of two possible problems:
The axes were large from the beginning, but showed small image with margins if the image is small enough
The command of showing the image that you are using is custom and it changes the axes size.
This question is old, but I stumbled across this (looking for something else) so perhaps it will help someone to see what I did.
I wanted to resize pretty large images (1024x 100k-200k pixels) so that my GUI can quickly demonstrate various color operations on a view of these large data sets. I just manually sub-sampled my data as follows (functions below).
Note that this example is an image. To spatially sub-sample a video, I have looped through the video and done something similar in the past on each frame.
[plotWidthPixels, plotHeightPixels] = getPlotAreaPixels(handles.figure1, handles.axes1);
[nSamplesPerLine nLines] = size(iqData);
colInds = decimateToNumber(nLines,plotWidthPixels);
rowInds = decimateToNumber(nSamplesPerLine,plotHeightPixels);
iqDataToPlot = iqData(rowInds,colInds);
First, I got the axis size in pixels:
function [plotWidthPixels, plotHeightPixels] = getPlotAreaPixels(figHandle, axisHandle)
set(figHandle,'Units','pixels')
figSizePix = get(figHandle,'Position');
set(axisHandle,'Units','normalized')
axSizeNorm = get(axisHandle,'Position');
axisSizePix = figSizePix.*axSizeNorm;
plotWidthPixels = ceil(axisSizePix(3)-axisSizePix(1));
plotHeightPixels = ceil(axisSizePix(4)-axisSizePix(2));
Then I used that to decimate the width and height of my image by getting sub-sets of indices that are (crudely approximately) evenly spaced:
function inds = decimateToNumber(lengthOfInitialVector, desiredVectorLength, initialIndex)
if nargin < 3
initialIndex = 1;
end
if (lengthOfInitialVector-initialIndex+1) > desiredVectorLength*2
inds = round(linspace(initialIndex,lengthOfInitialVector,desiredVectorLength));
else
inds = initialIndex:lengthOfInitialVector;
end
I have a question about the values returned by getPosition. Below is my code. It lets the user set 10 points on a given image:
figure ,imshow(im);
colorArray=['y','m','c','r','g','b','w','k','y','m','c'];
pointArray = cell(1,10);
% Construct boundary constraint function
fcn = makeConstrainToRectFcn('impoint',get(gca,'XLim'),get(gca,'YLim'));
for i = 1:10
p = impoint(gca);
% Enforce boundary constraint function using setPositionConstraintFcn
setPositionConstraintFcn(p,fcn);
setColor(p,colorArray(1,i));
pointArray{i}=p;
getPosition(p)
end
When I start to set points on the image I get results like [675.000 538.000], which means that the x part of the coordinate is 675 and the y part is 538, right? This is what the MATLAB documentation says, but since the image is 576*120 (as displayed in the window) this is not logical.
It seemed to me like, somehow, getPosition returns the y coordinate first. I need some clarification on this.
Thanks for help
I just tried running your code in MATLAB 7.8.0 (R2009a) and had no problems with image sizes of either 576-by-120 or 120-by-576 (I was unsure which orientation you were using). If I left click inside the image, it places a new movable point. It did not allow me to place any points outside the image.
One small bug I found was that if you left-click in the image, then drag the mouse pointer outside the image while still holding the left button down, it will place the movable point outside the image and won't display it, displaying a set of coordinates that are not clipped to the axes rectangle.
I'm not sure of what could be your problem. Perhaps it's a bug with whatever MATLAB version you are using. I would suggest either restarting MATLAB, or clearing all variables from the workspace (except for the image data im).
Might be worth checking to see which renderer you are using (Painter or OpenGL), a colleague showed me some wierd behaviour with point picking when using the OpenGL renderer which went away when using the Painter renderer.
Your code uses the Image Processing Toolbox, which I don't have, so this is speculation. The coordinate system is probably set to the figure window (or maybe even the screen), not the image.
To test this, try clicking points outside the image to see if you can find the origin.