Re: micro-manager-general Digest, Vol 37, Issue 15

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Re: micro-manager-general Digest, Vol 37, Issue 15

Fabrice Senger
Hi there and thank you for the infos,

this is more or less what I suspected even it is stated MM should work aswel with color camera.
What I think aswell is that there is a config file for the camera wich stores the last used parameters...so I will try to put the camera into BW mode...
I let you know if this works.

All the best,


Fabrice.

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> Today's Topics:
>
>    1. Re: Building MicroManager in linux (Daniel Jones)
>    2. Re: Problems with Leica Hardware (DMRA2 and        DFC Cameras)
>       (S. Pagakis)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 16 Dec 2009 23:49:32 -0800
> From: Daniel Jones <[hidden email]>
> Subject: Re: [micro-manager-general] Building MicroManager in linux
> To: Micro-Manager General
>         <[hidden email]>
> Message-ID:
>         <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Dec 16, 2009 at 5:21 PM, Nico Stuurman <[hidden email]> wrote:
>>
>> By the way, when I run ./mmUnixBuild I get the following message:
>> ./mmUnixBuild.sh
>> ...
>> libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and
>> libtoolize: rerunning libtoolize, to keep the correct libtool macros
>> in-tree.
>> ...
>> So maybe making a change to configure.in would eliminate this issue.
>>
>>> Done.
>
> I'm still getting this message when I run ./mmUnixBuild:
> ...(etc)...
> libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and
> libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
> libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
> ...(etc)...
>
> And running autoreconf gives me the same message. Still, as long as I run
>
> ./mmUnixBuild.sh
> autoreconf
> ./configure
>
> in that order, then ./configure seems to work fine for me.
>
>> So, now I can run ./configure without a problem. Unfortunately, when
>> I try to compile, I get the following error:
>>
>> make
>> ...
>> make[1]: Entering directory `/home/djones/src/micromanager1.3/mmstudio'
>> test -d build || mkdir build
>> rm -rf build/*
>> cp ./bin/plugins_mmstudio.config build/plugins.config
>> javac -source 1.5 -target 1.5 -sourcepath
>> ../MMCoreJ_wrap:./src:../hcs/src:. -classpath
>> /usr/share/imagej/../java/ij.jar:/usr/share/java/bsh.jar:/usr/share/java/swingx.jar:/bin/MMCoreJ.jar:. ./src/*.java ./src/org/micromanager/utils/*.java -d
>> build
>> ./src/org/micromanager/image5d/Image5D.java:658: cannot find symbol
>> symbol  : constructor LUT(java.awt.image.IndexColorModel,double,double)
>> location: class ij.process.LUT
>>           luts[i] = new LUT(
>> (IndexColorModel)chDisplayProps[i].getColorModel(),
>> chDisplayProps[i].getMinValue(), chDisplayProps[i].getMaxValue() );
>>                     ^
>> Note: ./src/org/micromanager/utils/JavaUtils.java uses unchecked or
>> unsafe operations.
>> Note: Recompile with -Xlint:unchecked for details.
>> 1 error
>> make[1]: *** [MMJ_.jar] Error 1
>> make[1]: Leaving directory `/home/djones/src/micromanager1.3/mmstudio'
>> make: *** [all-recursive] Error 1
>
> I'm not sure if a change was made, but I'm no longer getting this
> error since I re-checked out the source a little bit ago. Now when I
> run make everything seem to compile without a problem. Now we come to
> 'make install', which is a little more problematic. When I ran
> './configure', I used the following options:
>
> ./configure --prefix=/usr/local/ --with-imagej=/usr/local/ImageJ
>
> So basically I'm trying to keep everything in /usr/local and use a
> local installation of ImageJ (I also have ImageJ installed from the
> Ubuntu repositories. It may be a good idea to uninstall this, but it
> seems like what I'm doing here should work regardless). Unfortunately
> it seems like these options are more or less being ignored when I run
> 'make install'. For instance, all the shared object libraries are
> copied to /usr/lib/micro-manager instead of
> /usr/local/lib/micro-manager. Also, instead of copying all of the
> various *.jar files to /usr/local/ImageJ/plugins (or wherever would be
> appropriate for the local installation), 'make install' copies them to
> /usr/share/imagej. This is a problem because /usr/share/imagej is
> where plugins and such go for the Ubuntu version (i.e., from the
> repositories) of ImageJ, not the local installation that I want to
> use. The version in the repositories (1.41) doesn't work with the
> current version of Micromanager, which apparently requires ImageJ
> version 1.43.
>
> Maybe I'm making matters more difficult by having two installations of
> ImageJ, and I think I'll try uninstalling the version from the Ubuntu
> repositories. But still, it seems strange that the options I'm passing
> to configure are being ignored, unless I am missing something.
>
>
>>> One other note, I needed to install the boost c++ libraries in
>>> order to compile, but this library isn't listed on the wiki page
>>> (https://valelab.ucsf.edu/~nico/MMwiki/index.php/Linux_installation_from_source_(Ubuntu)) for Linux
>>> installation.
>
>> I updated that page, but it would be best if someone who is actually
>> building on Ubuntu could go over it and make sure that it all still
>> works.
>
> As you can see, I'm effectively in the process of doing that now. I
> think the mmscript on the wiki page may end up needing some
> modifications as well. Hopefully as I get this working any needed
> modifications can be made to the wiki page.
>
>
> Cheers,
> Daniel
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 17 Dec 2009 13:23:04 +0200
> From: "S. Pagakis" <[hidden email]>
> Subject: Re: [micro-manager-general] Problems with Leica Hardware
>         (DMRA2 and        DFC Cameras)
> To: Micro-Manager General
>         <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Fabrice
>
>
> I did followed some of the instructions found in e-mails in this list.
>
> In summary:
>
> The DFC Twain software from Leica was left where it was (in windows/
> twain_32) , but I downloaded the TWAINDSM.dll file and copied it into
> Windows/System32.
> For the DFC32 and DFC350 we have, the ds file it pick up is the DFC6.ds
>
> However,   if there are more than 1 ds files, it picks up the first,
> so the name needs to be adjusted so it picks up the right one.
>
> I also realised that the software works from the admin account but
> not from a noter "standard user" account, probably because of
> permission limitations.  it does give me a message about a "core
> property being read only".
>
>
> I also get the bit depth error with the DCFC320 (which is a colour
> camera) in colour mode.  In gray mode it works fine.  But I do not
> need it to work with MM (I really need the bw 350 for fluorescence)
> so I did not look more into it.
> PLEASE NOTE:  The bit-depth error does not depend on the MM operation
> (whether it is 8 or more bit ) as you mention but on the CAMERA
> operation (whether it is in colour or gray scale mode).  This
> parameter (also the binning) can not be set from within MM  but from
> within the Leica software ((which however CAN NOT operate
> simultaneously with MM).
>
>
> Hope it helps.
>
> S. Pagakis
>
> On Dec 16, 2009, at 8:31 PM, Fabrice Senger wrote:
>
>>
>>
>> Hi there,
>>
>> as I red, you managed to use the Leica camera...I red aswell you're
>> using a
>> DFC camera and I'm not sure this is the same as DC 300F ? But in my
>> hands,
>> everything works fine until step 4, I still get an error 22 :
>> problem with
>> bit depth, also I checked with the tawain software I'm working with
>> 8-bit...
>>
>> It looks as if, while going trough the initialization step the
>> program reads
>> some preferences and that this is messing up everything ?
>>
>>
>> What exactly was your problem with the camera and how do you
>> managed to fix
>> it ?
>>
>>
>> Thank you,
>>
>> Fabrice.
>>
>>
>>
>>
>>
>> S. Pagakis (IIBEAA) wrote:
>>>
>>> Dear Nico
>>>
>>> Thanks for the reply
>>>
>>> I did download MM and it looks as it is exactly what I needed.
>>> However, I had problems communicating both with our Leica Microscope
>>> (DMRA2) and all our Leica cameras (DFC350. DFC500 and DFC320) using
>>> the TWAIN interface.
>>>
>>> I will give here some info, in case someone could give me some
>>> pointers.
>>>
>>> The microscope works under MicrCtrl a small application which uses
>>> the Leica DM SDK library.  So there is an established communication
>>> through com1.  In case this created a conflict, I tried rebooting and
>>> NOT starting the Leica software before trying the MM.  No luck
>>>
>>> Also, all the cameras I tried work through the LAS Leica software.
>>> Therefore the drivers are present- not sure though whether I need to
>>> "link" them somehow with MM, or whether I should delete/disable the
>>> Leica drivers and let MM to use its own.
>>>
>>> Any help is greatly appreciated.
>>>
>>> Stamatis
>>>
>>>
>>> On Dec 4, 2009, at 3:48 PM, Nico Stuurman wrote:
>>>
>>>>> I noticed from the web site that you now (v1.3) support Leica
>>>>> cameras?
>>>>>
>>>>> I wanted to check this with you, before I start trying things.
>>>>>
>>>>> So we have a Leica DMRA2, a DFC350 and/or DFC500 firewire cameras
>>>>> and windows XP
>>>>> Will these work with the new veriosn so we can automate
>>>>> acquisition?
>>>>
>>>> Leica cameras work through the TWAIN interface.  It is a crippled
>>>> interface though, and things will work slow.
>>>>
>>>> Best,
>>>>
>>>> Nico
>>>>
>>>>
>
> *********************************
> Stamatis Pagakis Ph.D.
> Biological Imaging Unit
> Biomedical Research Foundation, Academy of Athens
> Soranou Efessiou 4, Athens 115 27 - Greece
> M:     +306946644955
> W:     +302106597481
> FAX: +302106597545
> http://www.bioacademy.gr/Faculty/core.php?cr=17
>
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call a beanshell from a macro?

Norbert Vischer-2
Hello All,

I was looking for a documentation how to call a beanshell script from the macro language; if this is possible, could someone give me a hint where to look for examples?

regards, Norbert
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Re: [micro-manager-general] call a beanshell from a macro?

Patrick Webster
So how was driving.  So I am trying to get focused on work and generally doing okay, and not think about having an aneurism and be found dead at my desk.  I don't like being mortal.  

LFP

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-----Original Message-----
From: Norbert Vischer [mailto:[hidden email]]
Sent: 2010-01-26 9:22
To: Micro-Manager General
Subject: [micro-manager-general] call a beanshell from a macro?

Hello All,

I was looking for a documentation how to call a beanshell script from the macro language; if this is possible, could someone give me a hint where to look for examples?

regards, Norbert
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Re: call a beanshell from a macro?

Nico Stuurman-4
In reply to this post by Norbert Vischer-2
Hi Norbert,

> I was looking for a documentation how to call a beanshell script  
> from the macro language; if this is possible, could someone give me  
> a hint where to look for examples?

With "macro language", I assume that you mean the macro interpreter  
build-into ImageJ?  If so, this can not be done.  On the other hand,  
you can call all ImageJ functionality (including macros - I presume)  
from Beanshell script, so you could probably structure your workflow  
that way.

I do like the idea of giving ImageJ macros the capability to call  
Beanshell code in Micro-Manager. We'll have a look to see what is  
involved in implementing.

Best,

Nico



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