Camera transpose correction

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

Camera transpose correction

PAVAK SHAH-4
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


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Camera transpose correction

nanthony

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: [hidden email]
Sent: Thursday, April 23, 2020 3:31 PM
To: [hidden email]
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

 



_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Camera transpose correction

Nico Stuurman-2
In reply to this post by PAVAK SHAH-4
Hi Pavak,

> 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.

Those properties were formerly used to determine camera orientation with
respect to the (XY) stage.  They have been retired since (and possibly
should be removed, but that can only be done once the C++ layers of MM
1.4 and 2.0 are no longer synchronized) in favor of affine transforms
(to set those, make sure to go through pixel size configuration).

As Nick mentioned, none of these affect the orientation of the image
itself.  The best thing for that is indeed the Image Flipper plugin.
Come to think of it, it is an interesting idea to have the Image Flipper
read the current affine transform.  Doing an actual affine transform
would be best, but that most often changes the image size with all kinds
of nasty consequences.

Best,


Nico




_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Camera transpose correction

PAVAK SHAH-4
Thanks for clarifying!

I used the image flipper, but was hoping to enable on-camera transpose to minimize overhead and maximize compatibility with some third party software that's less likely to be properly fixed. Not the end of the world for me, back to the flipper!

Pavak

On Thu, Apr 23, 2020, 3:06 PM Nico Stuurman <[hidden email]> wrote:
Hi Pavak,

> 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.

Those properties were formerly used to determine camera orientation with
respect to the (XY) stage.  They have been retired since (and possibly
should be removed, but that can only be done once the C++ layers of MM
1.4 and 2.0 are no longer synchronized) in favor of affine transforms
(to set those, make sure to go through pixel size configuration).

As Nick mentioned, none of these affect the orientation of the image
itself.  The best thing for that is indeed the Image Flipper plugin.
Come to think of it, it is an interesting idea to have the Image Flipper
read the current affine transform.  Doing an actual affine transform
would be best, but that most often changes the image size with all kinds
of nasty consequences.

Best,


Nico




_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Camera transpose correction

Nico Stuurman-2
Hi Pavak,

> I used the image flipper, but was hoping to enable on-camera transpose
> to minimize overhead and maximize compatibility with some third party
> software that's less likely to be properly fixed. Not the end of the
> world for me, back to the flipper!

Camera (adapter)s could offer this functionality (and the purpose of the
TransposeCorrection property may have been to indicate whether or not
the camera is executing the correction).  However, the camera api has no
unified
way to accomplish this (it probably should have!). Sorry!

Best,

Nico



_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Camera transpose correction

julou
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

--
Sent from: http://micro-manager.3463995.n2.nabble.com/


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
Reply | Threaded
Open this post in threaded view
|

Re: Camera transpose correction

nanthony
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


From: julou <[hidden email]>
Sent: Thursday, April 30, 2020 3:31 AM
To: [hidden email] <[hidden email]>
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

--
Sent from: https://urldefense.com/v3/__http://micro-manager.3463995.n2.nabble.com/__;!!Dq0X2DkFhyF93HkjWTBQKhk!AvXzukuMk-NgR4oLISgp4K0vLkVO_wsqlHxl4CQXskTDI_sYN0EWV3rVw01BdJ97ARJD_DoHG4w-$


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/micro-manager-general__;!!Dq0X2DkFhyF93HkjWTBQKhk!AvXzukuMk-NgR4oLISgp4K0vLkVO_wsqlHxl4CQXskTDI_sYN0EWV3rVw01BdJ97ARJD_NxIyXLt$


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Camera transpose correction

julou
Hi Nick,

I somehow overlooked your reply, sorry…
Very useful to know this distinction – and unfortunately not very user
friendly.

As much as I can very well imagine how development led to this state, it's
really a pity that camera transpose / flip are not stored along the
configuration, since as much as I can think off, this truly corresponds to
setup configuration settings.

I was thinking in the meantime what would be a convenient way to have both
the plugin and the configuration variables play nicely together (I mean in
the same UI)… what I came up with would be that whenever a corresponding
setting exists, it should be read at startup by the plugin and displayed as
"read-only" (e.g grated out and without interactions on click). Like this,
users would be reminded that corresponding actions are set in the
configuration but could add more on-the-fly action if they like. I hope my
description makes sense.

Best, Thomas




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

--
Sent from: http://micro-manager.3463995.n2.nabble.com/


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21