PS, just to give you an idea, those pictures were taken with a 4x lens and a 1.6um pixel size, larger than the rated 1um repeatability of our stage model... The overlap is of several microns. Like I said, I haven't had the time to be thorough with the system but I'll make proper measurements friday.


On 30 August 2011 18:21, Pedro Almada <> wrote:
Hi Nico and Jon,

I guess the first picture isn't very obvious, but all pictures from the position list show a consistent overlap, even though it was set to 0. My issue is that the slidescanner doesn't. Certainly, I'm guetting worse results now than when I had 1.3 installed (although I've yet to test this systematically. I'll have time later in the week).

On 30 August 2011 18:08, Nico Stuurman <> wrote:
Hi Pedro,

> I'm having an issue with the multi-position list on 1.4.5. I have calibrated my Prior ProScan II x,y stage with the automated pixel calibrator and have tested the Slide Scanner plugin successfully. However, when I try to use the "ROI>Position" function in the slide scanner window or the "Create Grid" function I always get overlapping pictures (even though I don't change the default 0 in the overlap option). The overlap seems to be of the same value.
> You can have a look through the following links:

What is the difference between the two datasets?

To be honest, even the first one does not look too bad to me.  It is difficult to move exactly to a given position, and the quality and settings of your stage and stage controller will have a big influence.  Linear encoders should really help, and you may need to tweak setting like your stage speed, acceleration, backlash correction, etc..  Even in the best cases, I have never seen reproducible, perfect (i.e. error < 0.5 um) positioning.

When there is a systematic error (the first dataset suggests that), most likely the pixelsize is incorrect (or at least, the stage's idea about pixel size does not correlate with your idea about pixelsize).



Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
micro-manager-general mailing list