[OpenSPIM] Anti-drift

[Aurelia Honerkamp-Smith]

Hi Luke,
Right!  I've never actually had the 'mouse moves stage' function working,
but thought it wasn't a big problem and used the stage controls tab
instead.  I have just found the 'Mouse moves stage' item that needs to be
clicked in the Tools menu, which I hadn't seen before, and did have to
transpose X and Y in my camera properties to get it to behave correctly.  I
think the X and Y transposition probably explains the interesting
"spiraling out of the frame" behavior I was seeing!  I'll try a timelapse
now and see if it works better. Thank you!
Aurelia



On Tue, Jul 22, 2014 at 6:07 PM, Luke Stuyvenberg <stuyvenberg at wisc.edu>
wrote:

> Hi Aurelia,
> On 07/21/14, Aurelia Honerkamp-Smith wrote:
> > Hello, First, I wanted to say that after last week's updates, the
> MicroManager error I was seeing on starting my camera is gone and
> configurations are loading correctly, so thanks for those! And, I have a
> question about the anti-drift function. Is it supposed to be autonomous at
> all, or does one need to be present, correcting the sample position for
> each timepoint? I had assumed that it was supposed to run on its own, but
> my samples always end up spiraling out of the field of view. Maybe I have
> inappropriate expectations of it? My pixel size is set correctly, and I
> don't know what else would affect it.
>
>
> In theory, the user shouldn't need to interact with it at all, though
> sometimes it helps to provide the first few corrections to get the sample
> in place. I've only seen it wildly overcorrect when the pixel size is
> missing/defaulted to 1... Could you possibly verify your pixel size
> setting, using Micro-Manager's 'mouse moves stage' feature? Try to drag a
> particular structure around in the view, making sure it follows the mouse
> pointer closely across the entire field of view. (You might need to flip
> the camera's view using properties in the Property Browser, if the stage is
> moving in the wrong direction.) I suggest this particular test since, at
> its basic level, this is precisely what anti-drift does: move particular
> features around to 'keep' their positions. Please also make sure that the
> pixel size you set is still in use after starting the OpenSPIM plugin, and
> that your configuration is saved with the correct pixel size set.
> (Importantly, also make sure that the property criteria set for your pixel
> size are being fulfilled by your setup -- usually the only property I
> specify is "Core-Initialize" must be "1".) One final idea is to try
> over-setting the pixel size slightly; this should reduce the offset size of
> the anti-drift somewhat.
>
>
> Barring this most likely possibility, the problem could also be something
> physical -- a motor snagging on its track or something like that,
> distorting the plugin's perception of position or interfering with the
> stage's ability to adjust its position. Alternatively, depending on the
> nature of the sample, the phase correlation may be having trouble
> automatically determining the offset (looking through the diffs directory
> might help). Another source of information may be the 'log.txt' file in the
> acquisition directory (though it is only made in the output directory of
> the first acquisition each time after the software is started);
> historically the plugin has logged the offsets applied to each view to that
> file.
>
>
> And of course, if you're okay with not getting any sleep, you CAN manually
> intercede at each timepoint. ;-)
>
>
> I'm sorry I can't immediately be of more help; ruling out pixel size
> leaves many equally unlikely explanations that are more difficult to
> verify. If you find the problem, or need more help, please feel free to
> write the list again; I'll see what I can do. Thanks,
> Luke
>
>
> On 07/21/14, Aurelia Honerkamp-Smith  wrote:
> > Hello, First, I wanted to say that after last week's updates, the
> MicroManager error I was seeing on starting my camera is gone and
> configurations are loading correctly, so thanks for those! And, I have a
> question about the anti-drift function. Is it supposed to be autonomous at
> all, or does one need to be present, correcting the sample position for
> each timepoint? I had assumed that it was supposed to run on its own, but
> my samples always end up spiraling out of the field of view. Maybe I have
> inappropriate expectations of it? My pixel size is set correctly, and I
> don't know what else would affect it.
> > Thanks,
> > Aurelia
>
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