The software currently has a user interface for multi-point magnification calibration, but does not implement anything using this data. Calibration data can be imported or exported in the form of a .csv table of {Magnification, HFOV} pairs. Separate calibration of horizontal and vertical pixel size is not currently supported.
The Open Beam Interface has no provisions for interfacing directly with a microscope's magnification scaling system. For some systems that have a serial port or external API, integrating automatic recording of magnification and other metadata will be easy but system-specific. In the generic case, the software depends on the user to type in the magnification.
Here's what I think is needed to support that:
Once the software knows what the current magnification is, the HFOV can be read or interpolated from the calibration points, and pixel size can be calculated. That information needs to be attached to saved images.
Seeing a scale bar with the image is also really useful context. I've implemented some related features before, but haven't brought it all together nor decided on a final form.
Here's what already exists:
A data bar in the image viewer is standard and should be implemented. I really enjoy customizing my data bars, but that can be done in a script and not through the GUI for now.
For reference, here's how an image is displayed with data bar in Zeiss SmartSEM software:
The saved image looks exactly like what you see on the screen. I like everything about how this works except covering the image with the data bar. I prefer to have the data bar below the image so 100% of the image is visible. I'm not sure whether the data bar is on a separate layer from the image in the saved tiff.
There's a lot of other metadata we should work on adding to images, but physical scale is absolutely critical context for interacting with image data and really needs its own treatment.
The software currently has a user interface for multi-point magnification calibration, but does not implement anything using this data. Calibration data can be imported or exported in the form of a .csv table of {Magnification, HFOV} pairs. Separate calibration of horizontal and vertical pixel size is not currently supported.
The Open Beam Interface has no provisions for interfacing directly with a microscope's magnification scaling system. For some systems that have a serial port or external API, integrating automatic recording of magnification and other metadata will be easy but system-specific. In the generic case, the software depends on the user to type in the magnification.
Here's what I think is needed to support that:
Once the software knows what the current magnification is, the HFOV can be read or interpolated from the calibration points, and pixel size can be calculated. That information needs to be attached to saved images.
Seeing a scale bar with the image is also really useful context. I've implemented some related features before, but haven't brought it all together nor decided on a final form.
Here's what already exists:
A data bar in the image viewer is standard and should be implemented. I really enjoy customizing my data bars, but that can be done in a script and not through the GUI for now.
For reference, here's how an image is displayed with data bar in Zeiss SmartSEM software:
The saved image looks exactly like what you see on the screen. I like everything about how this works except covering the image with the data bar. I prefer to have the data bar below the image so 100% of the image is visible. I'm not sure whether the data bar is on a separate layer from the image in the saved tiff.
There's a lot of other metadata we should work on adding to images, but physical scale is absolutely critical context for interacting with image data and really needs its own treatment.