How to map between microns and pixels?

[unimusic]

Hi, I am trying to extract patches from the original image based on the drawn contours by applying the inverse transform to the contour and placing it over the original image. However, we cannot find the ratio conversion between microns and pixels in the xml file.

How do we find the ratio between microns and pixels in the xml file? I can't seem to find the answer in the source code. Thank you!

• Angela

[k34harris]

If you have a calibration image, then you will be able to do the conversion following the procedures in the manual for calibration. If you know the size of your pixels you can enter it directly for calibration. You can also enter the pixel size at the time you import your images To get to this location you type series -- new series -- import -- images -- the Pixel Size : [image: image.png] Kristen *K <http://synapseweb.clm.utexas.edu>risten Harris* *915 Wild Basin Ledge* *Austin, TX 78746* *[email protected] <[email protected]>* *Personal Account*

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On Fri, Jun 19, 2020 at 1:37 PM Angela Zhang ***@***.***> wrote: Hi, I am trying to extract patches from the original image based on the drawn contours by applying the inverse transform to the contour and placing it over the original image. However, the x- and y- offsets are stored in microns, instead of pixels. How do we convert between microns and pixels? I can't seem to find the answer in the source code. Thank you! - Angela — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADHOUZX3GHY4AXAWDR2MAH3RXOV7RANCNFSM4OC6RDOA> .

[unimusic]

Sorry, I meant how to do it for data already imported into Reconstruct. It is old data from another source, so we don't know the information. How can we extract the information from Reconstruct?

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On Mon, Jun 22, 2020, 7:05 PM k34harris ***@***.***> wrote: If you have a calibration image, then you will be able to do the conversion following the procedures in the manual for calibration. If you know the size of your pixels you can enter it directly for calibration. You can also enter the pixel size at the time you import your images To get to this location you type series -- new series -- import -- images -- the Pixel Size : [image: image.png] Kristen *K <http://synapseweb.clm.utexas.edu>risten Harris* *915 Wild Basin Ledge* *Austin, TX 78746* ***@***.*** ***@***.***>* *Personal Account* On Fri, Jun 19, 2020 at 1:37 PM Angela Zhang ***@***.***> wrote: > Hi, I am trying to extract patches from the original image based on the > drawn contours by applying the inverse transform to the contour and placing > it over the original image. However, the x- and y- offsets are stored in > microns, instead of pixels. > > How do we convert between microns and pixels? I can't seem to find the > answer in the source code. Thank you! > > - Angela > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#3>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ADHOUZX3GHY4AXAWDR2MAH3RXOV7RANCNFSM4OC6RDOA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACRHM57ORA7OTQWTAKXBBC3RYAEUXANCNFSM4OC6RDOA> .