Grid creation issue in micro-manager

Usage & Issues
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#1

Hello, I’m new to uManager and seem to be having an issue with grid creation functionality. When I create a grid, with a certain overlap, the FoVs within a row overlap as expected but FoVs across columns do not overlap. I currently shift rows manually to make the grid work.

Any comments on this?

PS: I’m certain I’m using the right ‘pixel size’ as I determine this manually using a ruler slide. My stage is a Marzhauser, if this is relevant.

#2

Hi @orkun, welcome to this forum!

Does it so happen that your camera is rectangular rather than square? If so, you could have uncovered a bug, but please confirm before I start looking at that possibility.

#3

This is my camera;

#4

Instead of making me look at that documentation, can you please tell me if the image is a square or a rectangle?

#5

sorry, yes, rectangle.

#6

I just tried to reproduce this with the demo camera (by setting the image size to 756 x 512 pixels), but the output of the grid creator looks correct, and the same overlap is applied to both x and y.

  • Just to be sure, are you using a recent nightly build of 2.0?
  • Can you check that the y values in the generated list are correct (i.e. Pos_0001_0001 - Pos_000_000 equals image size for x and y minus overlap)?
#7

I’m using 2.0.0-beta3_20181129.

I was told that this is the stable version where the PointGrey camera drivers will work and newer versions do not yet have these drivers.

best
orkun

#8

The Spinnaker and Flycap2 device adapters are both included in the Micro-Manager installer, and will work with the version of the Point Grey driver as described in the documentation on the Micro-Manager website. Long ago, the Spinnaker device adapter was distributed separately, but that has long ago been remedied. So, please do try a newish nightly build and your troubles may go away;)