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image acquisition under linux

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image acquisition under linux

Aryeh Weiss
468 posts
I am wondering what open source software people on this list are using
to acquire time lapse images under linux.  At present, I only require
camera control,  and my camera is a Point Grey chameleon (USB 2.0),
which should work under libdc1394/libusb.

The obvious choice is micromanager, but I have been unable to get it to
work properly under Suse linux. I am trying to resolve that via the
micromanager list.

While I continue to bang my head against that wall, I thought that maybe
someone on this list has a solution, since I do not need all of the
capabilities of micromanager.

Thanks in advance
--aryeh
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Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

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Re: image acquisition under linux

Gabriel Landini
1783 posts
On Monday 08 Jul 2013 04:52:42 Aryeh Weiss wrote:

> I am wondering what open source software people on this list are using
> to acquire time lapse images under linux.  At present, I only require
> camera control,  and my camera is a Point Grey chameleon (USB 2.0),
> which should work under libdc1394/libusb.
>
> The obvious choice is micromanager, but I have been unable to get it to
> work properly under Suse linux. I am trying to resolve that via the
> micromanager list.
>
> While I continue to bang my head against that wall, I thought that maybe
> someone on this list has a solution, since I do not need all of the
> capabilities of micromanager.

Have you tried the Isight plugin? That is the only one I have been able to
make work with a number of usb webcams.

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Re: image acquisition under linux

Gabriel Landini
1783 posts
In reply to this post by Aryeh Weiss
...oops I sent before pasting the link.

http://fun.bio.keio.ac.jp/~funa/ij/

It works very well under opensuse 12.3 (64bit).

Regards

Gabriel

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Re: image acquisition under linux

Aryeh Weiss
468 posts
On 7/8/13 11:46 AM, Gabriel Landini wrote:
> ...oops I sent before pasting the link.
>
> http://fun.bio.keio.ac.jp/~funa/ij/
>
> It works very well under opensuse 12.3 (64bit).
>

Thank you for this suggestion.
I tried it, and it installs and runs with no problem.
Unfortunately, it does not recognize my camera.
Then again, libdc1394+libusb doesn't find my camera either.
However, lsusb ( utility that lists all connected USB devices)  finds
it, and lists all sorts of USB data for it.

Point Grey says that their USB cameras are IIDC 1394 compliant, so I am
stumped as to why I cannot get this camera work. Maybe Point Grey will
have the solution.

Best regards
--aryeh
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

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Opening a folder as stack

Richard Mort-2
21 posts
Hello All,
When I open a folder as a stack by drag and drop the files open in the
correct order. Also when I go file>image sequence> and select a random
image from the folder I get the same behaviour. However whan I use the
macro command:

dir = getDirectory("Choose directory");
run("Image Sequence...", "open=&dir starting=1 increment=1 scale=100");

or

file = File.openDialog("Choose a file");
run("Image Sequence...", "open=&file starting=1 increment=1 scale=100");


....my stack gets scrambled. I'm sure I'm missing something simple here
but maybe there is a better approach. My file naming is a bit odd and I
could relabel them all first but I have lots of images. Also the Stack
Sorter command "Sort by Label" works on the scrambled stack but it is
not recordable.

File name exmaple:

B16_F1_28_A_rec0000.modif.tif.0004.tif
B16_F1_28_A_rec0000.modif.tif.0005.tif

Hope someone can help
Best
R

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Dr Richard Mort
MRC Human Genetics Unit
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh.
EH4 2XU, UK

Tel: +44 (0)131 332 2471
Fax: +44 (0)131 467 8456


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Re: image acquisition under linux

Richard Kollmar-2
1 post
In reply to this post by Aryeh Weiss
According to Point Grey, their latest FlyCapture SDK, which includes a GUI capture program, works with their USB cameras under Linux: "With the release of version 2.0 of the FlyCapture SDK, users can program and operate Point Grey FireWire and USB imaging cameras in a Linux environment." (Knowledgebase Article 17: http://www.ptgrey.com/support/kb/index.asp?a=4&q=17&ST=usb+linux). They then refer to a Technical Application Note under Article 330: Getting Started with FlyCapture 2.0 and Linux.

In Article 17, they also describe steps to take for getting libdc1394 Support for USB Cameras to work. There is a very nice program to acquire from IIDC/DCAM firewire programs under Linux called Coriander (http://damien.douxchamps.net/ieee1394/coriander/) which has worked for us in the past with a PointGrey Grasshopper camera
(Firewire). As far as I understand, Coriander is based on libdc1394, but whether this is enough to make it work with your USB camera is above my paygrade.

Cheers,

Richard

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