micro manager

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

micro manager

Romain
Hi,

Is-it possible to implement micromanager in Bio7?
I used to use imageJ and micromanager (micromanager is an Image J plugin coming with his own imageJ version) together and I'm looking for a software able to connect them to R, what Bio7 does with ImageJ.

Thanks in advance,

Romain
Reply | Threaded
Open this post in threaded view
|

Re: micro manager

Bio7
This post was updated on .
Hello Romain,

i haven't worked with micromanager. The Reader however is an ImageJ plugin which can be dropped in the plugins folder of the Imagej plugin. It will be added to the plugins menu (see FAQ).

I can't say if everything will work correctly because i have no file for a test for the tabbed interface of Bio7 and i don't know the interface.

However the Micromanager app seems to use it's own interface and the ImageJ API.

So i think it could be possible to implemented it in Bio7 (i guess there a many native libs and *.jars involved which could cause some troubles)

But it would be some work beside licensing issues.

I will have a look at it at the weekend.
Reply | Threaded
Open this post in threaded view
|

Re: micro manager

Romain
Hello,

thanks a lot for your interest. The micromanager plugin for Image J is not enough for me. I need to take pictures from a camera connected on my microscope.

So I hope the implementation of micromanager in Bio7 could be possible. Bio7 is a damn good work anyway!

What I like in Bio7 too is the possibility to use it on Linux OS.

Sincerely yours,

Romain

 
Reply | Threaded
Open this post in threaded view
|

Re: micro manager

Bio7
In reply to this post by Romain
Hello Romain,

i installed Micro-Manager with the following results:

There are some problems with the tabbed interface.

1. Because of the different interface in Bio7 (in Bio7 a JPanel is directly embedded in the tabs) the Buttons occuring in an Micro-Manager image at the bottom are not available.

2. Two tabs are opened by default if you make a Snap from the current preview/display. This is related to the tabbed interface. In the windowed ImageJ a window is closed and the ImagePlus is added to a new window.
In Bio7 a new tab is created. IJ.hide() (ImageJ API) will not close the tab (so two tabs reference one image - if you close one both image references in the tabs are closed, too and an empty tab will be displayed).

3. The repaint of the preview only works if you click on the panel. I think the repaint mechanism is bound to awt (Bio7 uses swing, awt and swt) or the ImageWindow class of ImageJ. If you invoke the "Live" action you have to click on the panel to get an update. Please note that the second tab can be transferred e.g. to R.

4. The Album doesn't work because of the tabbed interface (a stack will be created which always adresses one ImagePlus object - see 2.)

Results:

It is at least possible to get an image from Micro-Manager.

Invoke Snap and transfer the second tab e.g. to R. For an update of the image always click on the first tab (it would be possible to write a script to repaint the image automatically).


How to install and test this:

1. Install MicroManager

2. Copy the *.dll and other files in the Micro-Manager base folder to the base directory of Bio7 (beside the Bio7.exe) except the the folders jre, macros, plugins and the files ImageJ.exe, ImageJ.cfg, ij.jar, IJ.prefs and unins00 (Copy the folders "mmautofocus", "mmplugins" and "scripts" in the Bio7 base directory, too!).

3. Copy the the Micro-Manager folder and Volume_Viewer.jar from the plugins folder to the ImageJ plugins folder of Bio7, path:

Bio7/plugins/com.eco.bio7.image_x.xx.x/plugins



If everything is in its place start Bio7. Micro-Manager can be found in the "Plugins" menu of the ImageJ view. As far as i could see the interface works fine and even the scripts are found and can be excecuted.

In Bio7 the ImageJ plugins are isolated from classpath of Bio7. Though BeanShell is part of a Bio7 distribution the Micro-Manager Beanshell *.jar doesn't make a conflict with the BeanShell *.jar of Bio7.

At all i was possitively suprised how far i came though the amount of native libs. It seems that paths in Micro-Manager are calculated from the base directory of an installation.

Of course i couldn't test it with real hardware but maybee at least it should be possible to get a picture from Micro-Manager.

For an improved image display the sources of Micro-Manager have to be patched to work with the tabbed interface of Bio7 and to display the buttons at the bottom of a MicroManager image/display.

Note: For the installation of Micro-Manager i used a Windows 64-bit OS! I also didn't look in the sources of Micro-Manager.






   
Reply | Threaded
Open this post in threaded view
|

Re: micro manager

Bio7
Multi-dimensional acquisition seems to work well. At least with time based data. The generated data is displayed as a stack in one tab.

Please note if you transfer data to R that you can controll your data with an R image plot.

If you transfer images as a double matrix simply select the data in the R-Shell and press the "Image" plot button in the "Plot Data" tab (image y-origin is displayed in the lower-left).