Re: [micro-manager-general] Camera transpose correction

[Nicholas Michael Anthony]

Hi Pavak,

 

There are some places in the code where these properties are used, but you are correct that they don’t actually affect the images from the camera. If you want to actually rotate the images you might look at the “Image Flipper” which is one of the “On-The-Fly” plugins, this will affect the way that images are displayed and saved.

 

One place that comes to mind where the Mirror, Transpose, etc. properties are used is the automatic “Pixel Size Calibrator”. Since it needs to correlate motion of the XY stage with motion seen on the camera it uses these properties.

 

It would be great to have the “Image Flipper” functionality and the Transpose/Mirror  properties that you mention all unified into a single mechanism but if I’m not mistaken it would require some serious overhauling of how cameras are handled in Micro-Manager.

 

--Nick

 

Sent from Mail for Windows 10

 

From: PAVAK SHAH
Sent: Thursday, April 23, 2020 3:31 PM
To: Micro-Manager General
Subject: [micro-manager-general] Camera transpose correction

 

Are the camera transpose correction properties ignored in 2.0g or have I missed a key step in enabling them? Setting TransposeCorrection, MirrorX, Mirror, or TransposeXY has no effect on the images.

 

Thank you!
Pavak

 

[Nicholas Michael Anthony]

Hi Thomas,

The way that the code is currently structured means that the On-The-Fly plugin settings are stored in the "User Profile" rather that the "Hardware Configuration". Obviously, in cases like this that is not ideal but I think it would be non-trivial to fix this.

The solution that I use is that for every hardware configuration I also create a new user profile by the same name. By always using each configuration with it's own user profile I effectively have unified settings for each hardware configuration.

--Nick

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From: julou <thomas...@normalesup.org>
Sent: Thursday, April 30, 2020 3:31 AM
To: micro-mana...@lists.sourceforge.net <micro-mana...@lists.sourceforge.net>
Subject: Re: [micro-manager-general] Camera transpose correction

 

Hi,

This brings me to a question: is it possible to save settings of on-the-fly
processing in the config file? (or maybe it is already and I overlooked it)…


Nico Stuurman-2 wrote
> Come to think of it, it is an interesting idea to have the Image Flipper
> read the current affine transform.

Indeed, I do't know whether it would be doable in practice (in particular if
some camera DA use this setting while other don't). But if it is, the twould
be very handy!!

Best,
Thomas




-----
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21

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