[OpenSPIM] Open Spim Questions

[Johannes Schindelin]

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