This micrograph taken from standard sanga stage.
The motors are functioning smooth. But I have this issue of white spot .I have tried cleaning the sensor, tube lens, the objective. Nothing seems to work. Is there something I could do to remove that spot?
I have one more query regarding the capture function.What would be the ideal step size (X,Y,Z) if I have to scan a slide of 1.5cm x 1.5cm for subsequent stitching?
Have you run the camera calibration again after cleaning the optics? Settings → Camera → auto-calibrate
The white spot looks to be the effect of a correction for a dark dirt spot, which has now been removed by your cleaning.
For a slide scan it depends on the field of view of the lens that you are using. You will need to have overlap between images if you want to stitch the final image set together. You can find how many steps in x and y give a sensible motion by trial moves, or by looking at the .json file that includes the camera stage mapping information if you have run that process.
The full range of motion of the stage is not really quite enough for a full 15mm x 15mm scan. For large scans you will need to be careful of the limits of your stage and how many steps are needed to get there, and make sure that you are always starting in the right place. There is currently no automatic detection of centre or of the mapping of steps to physical distance in the microscope. Both are under discussion but are not likely to be implemented very soon.
Thanks,I will try calibrating again.
Again thanks for the useful information on the step sizing and related protocols.
The Camera stage mapping can be easily downloaded using Settings → Camera/Stage mapping → Download calibration data
A couple of other threads here on scanning, home and limits and linking steps or camera pixels to real distance:
How to define scan area? - Request Help - OpenFlexure Forum
Home / Limit switch - Contributions - OpenFlexure Forum
Microscope resolution / target reference samples - General - OpenFlexure Forum
The bright spot is sometimes caused by a misaligned condenser, or by not using a diffuser in front of the LED. Did you use electrical tape or PTFE tape in front of the LED? Are you using a condenser lens?
spot on…I am not using any condenser lens.
thanks
no worries - though actually I have seen a bright spot like that more often when people are using the condenser, but not using a diffuser.
A quick if slightly hacky fix is to put a piece of thin white tape or paper where the condenser lens should be. This will give a less spatially coherent illumination, at the cost of not being quite as bright. I’ve not done this in a little while, so I’m not sure if the current condenser will work well this way (because of the distance between the LED and the sample) - if you have a moment to try it, I’d be interested to hear how you get on.
