Applying Gaussian 3D filter to 32 bit float 3D Micro-CT image

2 次查看（过去 30 天）

Hege 2020-10-10

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/610276-applying-gaussian-3d-filter-to-32-bit-float-3d-micro-ct-image

评论： Hege 2020-10-20

Hi All,

I have a Micro-CT data file to process it through Matlab as shown in below. My array is a 3D array and it is 32 bit float. but gaussian filters which are introduced in mathworks are not supported to float data type

fid = fopen('E:\RE\re_C_7mm_6um_1d42s_01\re_C_7mm_6um_1d42s.vol');
voxels = fread(fid, '*float32');  %read as 32 bit float. I'm assuming they are 32 bit float(CT data)
fclose(fid);
voxels = reshape(voxels,[1920,1920,1536]);
d=imbinarize(voxels,95); % Thresholding the volume
d1=imgaussfilt3(d)  % This  lines gives me an error that it supports only for uint,int, single or double.check the error

What I should do to filter my 3D array using the gausfilt3 command? Appreciate your valuable advices. I want to remove the P(see the attached image)with or without gausfilt3.Appreciate your valuable adivces!

Error is shown below. A is the file for the filtering. If you check the gaussfilt3 command in mathworks A is defined. it is not my own name.

Error using imgaussfilt3
Expected A to be one of these types:
uint8, uint16, uint32, int8, int16, int32, single, double
Instead its type was logical.
Error in imgaussfilt3>parseInputs (line 285)
validateattributes(A, supportedClasses, supportedImageAttributes, mfilename, 'A');
Error in imgaussfilt3 (line 116)
[A, options] = parseInputs(args{:});
Error in volreading (line 55)
d1=imgaussfilt3(d)
 

0 个评论
显示 -2更早的评论隐藏 -2更早的评论

请先登录，再进行评论。

请先登录，再回答此问题。

回答（1 个）

Image Analyst 2020-10-11

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/610276-applying-gaussian-3d-filter-to-32-bit-float-3d-micro-ct-image#answer_510521

Try imfilter() with your own custom kernel that is a Gaussian shape.

11 个评论
显示 9更早的评论隐藏 9更早的评论

Hege 2020-10-12

Thank you very much Image Analyst!

I tried regionprops3() and I received a huge set of data(Please see the attached image. I attached a small portion of the table as the table size is 863618x3 table. Reason is fibers are broken.That is why I received this amount of voxels.Actually, I want to remove the cylindrical shape(P) and the sample holder. So, I am thinking about these voxels numbers to identify and how to remove it. But I noted that only one voxel value has 311793705(first value in the image table).Others are comapratively small. If you check the image you will notice it.Thinking how I should use the table to remove the unwanted things using these values.

Actually, doubt in my head is, I generated the table using below commands.

d=imbinarize(Micro-CT file,114.6);

e=regionprops3(d);

but in the table there voxel values less than 114.6 as well.something 1,2 etc.

In the mean time, I found an experimental solution but worrying how I should apply it to the 3D Image. If I can binarize the voxels between 114.6-220 clearly, I can remain the fibers and others are gone.Something like a badpass filter.What I am trying to say is I want the voxels between 114.6 and 220. As a result of this, voxels out of the margin should be zero. Basically, thinking about how to apply a lower threshold value and upper threshold value to my 3D array.

Any of your suggestions are highly appreciated!.Thank you in Advance.

Hege 2020-10-15

Thank you Image Analyst.

Honestly, I tried the d=double(voxels) command first. may be then something wrong in my script.

Actually, what I am trying to do is ,voxels values more than 95 should be 1 and if not it should be zero. Further, voxels values less than 220 should be 1 and if not it should be zero. That is what I am trying to do at the moment. Appreciate if you can show if there is any mistake of way I am trying to do thresholding.Thank you

Hege 2020-10-20

Thank you for your support Image Analyst. I thresholeded the 3D volume and heading for the skeletonization. But I got the values from Micro-CT experimental works. Thank you in Advance

请先登录，再进行评论。

请先登录，再回答此问题。

类别

Image Processing and Computer Vision Image Processing Toolbox Image Filtering and Enhancement Image Filtering

在 Help Center 和 File Exchange 中查找有关 Image Filtering 的更多信息

产品

版本

R2020a

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by