[OpenSPIM] Open Spim Questions

Thu Aug 27 05:07:58 CDT 2015

Hi,

I can only help with point 3.

The newest version of the code is her:
https://github.com/openspim/SPIMAcquisition
As far as I remember, the procedure is to install Fiji and then switch 
on the OpenSPIM update site, then Fiji will install the newest version 
automatically. I was doing some minor changes to the plugin and then 
doing as that page says: building my own plugin, replacing the plugin in 
the Fiji directory. Last time I did it I used jdk1.8.0_51 and it worked.

Regards,
Monika

W dniu 2015-08-27 10:18, Johannes Schindelin napisał(a):
> Hi Evangelos,
> 
> I am replacing the obsolete OpenSPIM mailing list address with the one
> that we use since May 2013, so that the OpenSPIM mailing list
> subscribers can see it.
> 
> Ciao,
> Johannes
> 
> On 2015-08-26 20:29, Evangelos G. Gatzogiannis wrote:
>> Dear Peter and OpenSpim team,
>> 
>> In brief, I have built a custom light-sheet microscope based off of
>> micromanager.  Future experiment will focus on early embryos and need
>> high speed imaging and fast rotation with 2 cameras.
>> 
>> I have a few detailed questions that could help make OpenSpim even
>> more versatile by supporting faster Physik Instrumente hardware, such
>> as for early embryos and fast developing small organisms.
>> 
>> I appreciate any comments and help, as described below.
>> 
>> 
>> Is it  possible that OpenSPIM only needs minor enhancement to allow
>> the use of Physik Instrumente hardware for 4-D positioning? I would
>> like to use PI Hera piezos PI-Hera P-629.1CD and PI U-628.03 rotation
>> for moving sample through the sheet, and rotating the sample, in
>> addition to an x stage PI Z-522.040 for repositioning the sample in z.
>> These are faster, more precise and have less hysteresis and backlash
>> than existing motors.
>> 
>> 
>> 
>> ----
>> 
>> We are using Micro-Manager on a 64-bit Windows 7 platform to build a
>> light sheet microscope. We are interested in trying OpenSPIM since its
>> write-up indicates that it addresses issues that face us. One issue is
>> handling loss of focus when rotating a specimen. The other is drift.
>> 
>> 
>> 
>> Our application positioning the specimen in X, Y, and Z, and rotating
>> it (in axis Theta). The mount for our specimen requires that we treat
>> the Y axis a Z, and the Z axis as Y.
>> 
>> 
>> 
>> Our goal is dual-camera acquisition of Z-series at multiple angles of 
>> rotation.
>> 
>> 
>> 
>> For proof of concept with Micro-Manager, we are using a Physik
>> Instrumente C-884.4D stepper motor controller with the Physik
>> Instrumente GCS-2 device adapter, which we have configured to work
>> specifically with the C-884.4D controller. The result works, but (a)
>> rotation is too slow, and (b) slewing in our "Z" axis is too slow. We
>> must replace that controller and the stepper motors. Physik
>> Instrumente has offered us a (fill in) controller.
>> 
>> 
>> 
>> To our knowledge, we face these problems:
>> 
>> 
>> 
>> 1. Constraint in choice of hardware. Micro-Manager (and therefor
>> OpenSPIM) does not allow one to treat two linear stages as an X-Y
>> stage using arbitrary single-axis controllers or using one axis of a
>> multi-axis controller. Unless that is changed, our choices of vendor
>> are limited. Physik Instrumente implements a scheme in which for the X
>> and Y axes one specifies the controller that is used. If we do not use
>> a Physik Instrumente controller, we are restricted to a controller
>> that implements a similar scheme, or we must use a controller that
>> implements all the axes.
>> 
>> 
>> 
>> 2. We know that OpenSPIM is written for a Picard Industries
>> USB-4D-Stage. It appears that the SpimAcquisition plugin includes
>> specific code for interfacing the Picard USB-4D's Z-Stage, X-Y Stage
>> and Rotator (its Theta axis). We would need analogous code to allow us
>> to use the controller or controllers on which we settle. Links below
>> show the specific code for the Picard USB-4D, written in Java.
>> 
>> 
>> 
>> How complicated would it be for us to extend OpenSPIM to allow us to
>> use four axes of Physik Instrumente devices for our purpose?
>> 
>> 
>> 
>> 3. We would try modifying the SPIMAcquisition plug-in ourselves, but
>> the documentation for OpenSPIM leaves us wondering about the version
>> of the Java SE Development Kit that is required. The documentation for
>> Micro-Manager indicates that OpenSPIM is built with the Version 1.6
>> Development Kit, which is outdated at this point - the latest release
>> is version 6u45. Would we run into trouble using the Version 1.8 ?
>> 
>> 
>> 
>> 
>> 
>> 
>> I greatly appreciate your comments and help.
>> 
>> Best,
>> Evangelos
> 
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