Image magnification and tiling

Dear Guru
I was successful to use TileExporter in Qupath Version: 0.2.3 with image.svs.
It is working properly.
My pre-processing is to magnify the image (20x objective lense) then make tilling before passing to another detection program.
Can you give me some advice in the particular script?
Can you guide me in the steps,the magnification script can use within TileExporter
or it shoud work solely before TileExporter.
Thank you very much
Banatus Soiraya

Sample image and/or code

  • Upload an original image file here directly or share via a link to a file-sharing site (such as Dropbox) – (make sure however that you are allowed to share the image data publicly under the conditions of this forum).
  • Share a minimal working example of your macro code.

Background

  • What is the image about? Provide some background and/or a description of the image. Try to avoid field-specific “jargon”.

Analysis goals

  • What information are you interested in getting from this image?

Challenges

  • What stops you from proceeding?
  • What have you tried already?
  • Have you found any related forum topics? If so, cross-link them.
  • What software packages and/or plugins have you tried?

The size/magnification/resolution is handled by the downsample value with the TileExporter: https://qupath.readthedocs.io/en/latest/docs/advanced/exporting_images.html#tile-exporter

In general, it’s best to avoid basing any analysis decisions on magnification values (e.g. 20x) because these can be completely different depending upon the scanner – pixel size is more consistent (and downsample can be calculated from that). See here for more info:

Hi Petebankhead
Appreciated for you help.
Now, i tried to use Tile Exporter
I tried to use tileSize(2592) then size of each tile tile became 25922952 equally.
Q1:However I need 2592
1944 How do I define in tileSize(xx,xy)?
Q2: I deceased a parameter (requestedPixelSize ) from 5.00 to 0.15 in order to equate cell and nucleus in another system It looked pretty good if compare between the existing image and the
Q3: Can you explan more about requestedPixelSize,pixelSize ,downsample(downsample)?
Q4: About magnification 20x, How many parameters inTile Exporte that should be adjusted?
Please kindly give me some advice.
Thank you
Banatus Soiraya

Use tileSize(2592, 1944)

‘Pixel size’ is the resolution at which the image is scanned (displayed under the ‘Image’ tab).
‘Requested pixel size’ is the resolution you’d like for the output.
‘Downsample’ is the result of ‘Requested pixel size’ / ‘Pixel size’.

I recommend setting the requested pixel size. As described above and in the previous link, magnification is not standardized; a 20x image on an Aperio scanner might have a completely different resolution (pixel size) from a 20x image on a Zeiss scanner.

Even with the same scanner or microscope model, there might be variations if different cameras are used; it is not a good idea to define things in terms of magnification.

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