Adipose tissue analysis in breast cancer

Hello everyone,

I am new. I am starting to analyse adipose tissue in slides (H&E) of breast cancer.
My first question is how to convert NDPI files in a format suitable for an analysis with adiposoft without loosing resolution?
I tried to use NDPI tools as well as NDPI converter, but the result is unsatisfactory. The quality of new format is very low and I can’t zoom the image. Maybe a solution could be select only an area of the whole image?

My second question: Is there a tutorial that describe step-by-step how to analyse adipose tissue ?
I read the article of Gallaraga about adiposoft, but there are certain passages not so clear for me.
I need to calculate the number of adipocytes, the area and the diameter of each individual adipocytes.

Hi @InfiniteJest,

You can use the BioFormat plugin. Here is a script to help you manage this files :

run("Bio-Formats Macro Extensions");
numSerie = 1; // 1 for full resolution, 2 for half resolution, etc.

dir = getDirectory("Choose the image directory");
list = getFileList(dir);

for (i=0; i<list.length; i++)
{
   if (endsWith(list[i], ".ndpi")>0) //for .ndpi files
   {
      path= dir+"\\"+list[i];
      NameImg = list[i];

      Ext.setId(path);
      Ext.getSeriesCount(seriesCount);

      for (s=0; s<seriesCount; s++)
      {
         Ext.setSeries(s);
         Ext.getSizeX(sizeX);
         Ext.getSizeY(sizeY);
         Ext.getSeriesName(NameSerie);
         Index = indexOf(NameSerie, "Series " + numSerie);

         if (Index >= 0) //this is the good series
         {
            run("Bio-Formats Importer", "open=[" + path + "] autoscale color_mode=Default split_channels view=Hyperstack stack_order=XYCZT series_" + numSerie);

   	   selectImage(NameImg + " - Series " + numSerie + " - C=0");
   	   rename("C0");
   	   selectImage(NameImg + " - Series " + numSerie + " - C=1");
           rename("C1");
           selectImage(NameImg + " - Series " + numSerie + " - C=2");
   	   rename("C2");
         }
      }
   }
}
Ext.close();

Then you can segment the walls. When you invert the image, you will get the adipocytes and you can measure them.

Nico

Thanks for your help @VirtualSlide.

When I launch the script in Macros --> Run, there is an error message

*Undefined variable in line 23. *
Index = IndexOf ( , “Series” + numSerie):

You are true @InfiniteJest , I forgot to translate variables from my french program :slight_smile:
I edited the message. you have to replace the former NomSerie with NameSerie and NomImg with NameImg

Nico

Thanks again @VirtualSlide

But I have another error:

Error: “Example1.ndpi - Series 1 - C=0” not found in line 29:
selectImage ( NameImg + " - Series " + numSerie + <" - C=0"> ) ;

Edoardo

Hi @InfiniteJest,

The code is working on my PC. Do you work on a mac ? (in this case, replace path= dir+"\\"+list[i]; with path= dir + File.separator + list[i];).
The other solution might be that your image is too big (>2GB) to be opened at full resolution in Fiji. You have to crop it to process it or to use a lower resolution : numSerie = 2;// or 3 or 4... .

Nico

1 Like

Yeah. The problem was the resolution. My images are too big, so I set to a lower resolution (2), and now it works.

Many thanks for your help @VirtualSlide
Now I can start with the analysis of adipocytes.
I am reading the manual of ImageJ. But my question, is there a tutorial for adipocytes analysis ?

Hi Edoardo,

I usally segment the walls with a Triangle segmentation and remove artefacts with mathematical morphology.

To compare images, we compare the distribution of adipocyte size.

Nico

Hi Nico,

I started to use adiposoft for the analysis of adipocytes.
Do you know how adiposoft compute the diameter if the adipocytes are not a perfect circle?
And in Image J is there a tool with a measuring stick?

Because I tested adiposoft vs a software (HALO) that I am currently using and there is a constant difference between the two software in detecting the measurements of diameter and area.
Difference that getting bigger with the increase of adipocyte size.

Many thanks

Edoardo

Hi Edoardo

I’ve send you a PM. If you want, I can analyse a few of you images with my own method and tell you wich sizes I find, so you can compare wich of the software is the best.

Nico