Add points to 3D image

Question

I have 2D image data set for 3D image. Since my data is very large, in this question, I use sample data.

testdata = Import["ExampleData/CTengine.tiff", "Image3D"];
sl = Image3DSlices[testdata];

(The the structure of my own data is same as "sl".)

Now, I want to color certain pixels (in the different color from the "sl" depicting color) of 30th picture in the 2D positions of

{{25, 30}, {27, 32}, {26, 31}}

100th picture in 2D positions of

{ {{63 ;; 65}, {42 ;; 45}}, {150, 70}, {{200 ;; 205}, {230, 234}} }

250th picture in 2D positions of

{{12, 90}, {100, 180}, {3, 48}, {230, 250}}

So I made another 3D data set for depicting spots as

SpotdataForEachz = Table[Table[0, 256], 256];
stack = Table[SpotdataForEachz, 256];   

stack[[30]][[25]][[30]] = 1;
stack[[30]][[27]][[32]] = 1;
stack[[30]][[26]][[31]] = 1;

stack[[30]][[63 ;; 65]][[42 ;; 45]] = 1;
stack[[30]][[150]][[70]] = 1;
stack[[30]][[200 ;; 205]][[230 ;; 234]] = 1;

stack[[100]][[12]][[90]] = 1;
stack[[100]][[100]][[180]] = 1;
stack[[100]][[3]][[48]] = 1;
stack[[100]][[230]][[250]] = 1;

stack[[250]][[12]][[90]] = 1;
stack[[250]][[100]][[180]] = 1;
stack[[250]][[3]][[48]] = 1;
stack[[250]][[230]][[250]] = 1;

ima = Image[#] & /@ stack;

Then I tried to overlay

Overlay[{Image3D[sl], Image3D[im]}]

However it didn't work. Also, I think there might be a better way of doing this. Does anyone have nice idea for this problem?

Answer 1

You can't directly reassign the value of a pixel in an Image object using Part ([[ ... ]]). Instead, use ReplacePixelValue. For instance, for your first specification you could write:

ReplacePixelValue[sl[[30]], {{25, 30}, {27, 32}, {26, 31}} -> 1]

To avoid repeated typing, you can wrap it all in a MapThread expression, giving it a list of images to be modified, and a corresponding list of modifications for each image. The function being applied to each pair modifies each specified 2D slice in place inside sl, leaving th.

testdata = Import["ExampleData/CTengine.tiff", "Image3D"];
sl = Image3DSlices[testdata];

MapThread[
 (sl[[#1]] = ReplacePixelValue[sl[[#1]], #2 -> 1]) &,
 {
   (* list of images to modify *)
   {1, 80, 100},
  
   (* list of positions to modify in each image *)
   {
     {{63 ;; 90, 10 ;; 50}, {150, 70}, {230, 234}}, 
     {{25, 30}, {27, 32}, {26, 31}},
     {{12, 90}, {100, 180}, {3, 48}, {230, 250}}
   }
 }
]

Finally, you reconstruct a 3D image by feeding the modified list of slices to Image3D:

Image3D[sl]

Note that in the code above I changed the list of images so it would work with your sample data (which only contains 110 images). Your list of modifications also contained an inconsistent specification ({{200 ;; 205}, {230, 234}}) which I didn't know how to interpret, so I dropped it. Otherwise this should be straightforward to apply to your own image stack.