Dear image people,
I’m seeking to extract the correct stage center position of a tiled 10x fluorescence scan that is saved in the .czi format. If I open this file in the ZEN software, I get the following readings:
The value “Image Center Position” is the value I would like to extract automatically with an ImageJ macro script. However, I can find this value nowhere in the metadata. The marked entry seems to contain the center position:
which obviously doesn’t match the coordinates above in the readings of the ZEN software. Anything I’m overlooking?
For context, here’s what I’m trying to do: I have a 10x overview image with some few 40x detail scans that are spread across the whole slice. I did some analysis (quantification, registration, etc) on the 10x image and I would like to trace the position of the 40x images through this process.
Thanks in advance for any help!
The same occurs for the (tiled) 40x images, for which ZEN tells me
whereas Fiji tells me
The two values are closer to each other in this case, but still do not coincide perfectly.