DRBIO MultiPhoton Microscope

Installing CCS Tools on PC

2010-12-07T17:18:00.013-05:00

We use Custom Computer Services (CCS) software development tools to compile and build embedded programs that control the custom printed circuit boards in the lab. The PIC and SX microcontrollers are the main programmable units used to drive the circuit boards. The necessary CCS development tools can be found in DRBIO's ftp site under the directory called CCS_Compilers

Here's the installation guide for the CCS programs.

Lumencor RS232 Control

2010-09-02T23:10:00.000-04:00

The past few days, I’ve been working with Paul to write a C++ program to communication with the Aura Lumencor Light Engine via the computer’s RS-232 port. Warren provided a COMMDRV library (http://www.wcscnet.com/), which includes functions for RS-232 communication. The most critical functions for the project were ‘PutByte’ (which allows for the transfer of a single character), ‘OpenComPort’, ‘SetPortCharacteristics’ (to set baud rate, parity, stop bits and communication protocol) and ‘CloseComPort’. Since the Lumencor specification (http://www.lumencor.com/downloads/Aura%20TTL%20IF%20Doc.pdf) expresses byte sequences in hexadecimal, we used ‘PutByte’ to pass unsigned char’s represented as hex (e.g. unsigned char byte1 = 0xff). One issue that we ran into was that the program processed all the bytes and terminated much more quickly than the serial port could pass the data to the Light Engine. This led to the truncation of many of the commands. In order to correct for this, we added ‘Sleep’ commands so that the program would wait long enough to allow data transfer.

A few notes on the COMMDRV library. In order to use the library functions, the cdrvhf32.lib and cdrvxf32.lib files must be included in the program. In addition, <comm.h> must be included and ‘MSWIN’, ‘MSWIN32’ and ‘MSWINDLL’ must be defined. The omission or incorrect placement of these declarations may lead to link errors; try to include them as early as possible in the program.

One very useful tool for debugging RS-232 communication is a terminal emulator such as Hyperterminal or Realterm; I preferred the layout of the latter. By connecting two COM ports (whether on different computers or on the same computer) via a NULL MODEM cable, you can pass bytes and check to see how they are received on the other end; the NULL MODEM cable serves to cross the transmit and receive pins of the two RS-232 cables (so that receive(COM1) à transmit(COM2) and transmit(COM1)àreceive(COM2)). Note: NULL MODEM cables have the same pin structure as RS-232 cables and can come in various male / female configurations. Be sure to look for the NULL MODEM label!

In order to create short hex files containing Lumencor commands, I used the HxD hex editor. The hex files could be dumped to the COM port using RealTerm.

PCI-1755 DAQ Tip

2010-02-15T11:44:00.008-05:00

This PCI-based card manufactured by Advantech is the high speed 32-channel digital I/O device used for the multiphoton image acquisition system. It has an extra general-purpose 8-ch DI/O feature that comes in handy. However, make sure to flip the on-board 8-pin switches in order to designate individual pins DI or DO. This is something that is easily overlooked and caused confusion for me.

Project Build error in Visual Studio 2005

2010-01-19T14:04:00.003-05:00

I came across the error "SignTool Error:ISignedCode::Sign returned error: 0x80880253 The signer's certificate is not valid for signing." when trying to build/publish my VB code in Visual Studio 2005. I know a few people in the lab also use VS2005, so I'm posting how to get around this error in case you come across the same thing.

The first time you publish your solution, VS creates a certificate that expires in one year. If you try to update your solution or re-publish over a year later, you will probably get the error mentioned above. Microsoft explains this problem and gives a fix for it here... http://support.microsoft.com/kb/925521

I did not get the Microsoft fix to work for me, but I was able to work around it as follows.
Go to Project -> Properties -> Signing Tab.
Click "Create Test Certificate"
Enter a password
Click "OK"

This doesn't exactly fix the problem, but it extends your certificate for another year so that you can publish your project.

FCS Bin Size - Board #1 (Revised)

2009-12-17T11:52:00.008-05:00

The FCS counter board #1 (used by Phill Jones) has been re-flashed with updated firmware to allow one- or two-channel data acquisition mode.

The bin sizes for one-channel mode are 0.479 μs, 0.998 μs, 1.995 μs and 4.989 μs. For two-channel mode it's 0.818 μs, 0.998 μs, 1.995 μs and 4.989 μs.

FCS Bin Size - Board #2

2009-11-17T17:02:00.015-05:00

New FCS hardware and firmware now provide the FCS application-level software the option of choosing one or two data channels. Lisa measured and verified the actual time bin sizes generated from the new board.

The bin sizes for one-channel mode are 0.4801 μs, 1.0002 μs, 2.0003 μs and 5.0007 μs. For two-channel mode, the values are 0.8201 μs, 1.0002 μs, 2.0003 μs and 5.0007 μs.

FCS Bin Size - Board #1

2009-11-03T14:10:00.006-05:00

The FCS software provides four different user-selectable bin sizes. Nominally, the available bin sizes are 0.8 μs, 1 μs, 2 μs, and 5 μs. The actual bin sizes will be slightly different because of how they are calculated in the firmware. (I will go into more detail on this below.) In reality, the bin sizes used by the software are 0.818 μs, 0.998 μs, 1.995 μs, and 5.009 μs.

The FCS hardware is controlled with an SX48 microprocessor, and the different bin sizes are generated by adding or removing instruction cycles to the SX code. The SX uses a 50MHz crystal, so each instruction cycle is 20 ns. These actual bin sizes are the closest we could get to the ideal values given the 20 ns resolution. The code for the 0.818 μs bin size has no delay cycles added, so this is the smallest possible bin size.

Code Profiler for Windows

2009-09-16T12:08:00.019-04:00

Very Sleepy is a nifty little C/C++ profiler. It's been useful for me in code development. Plus, it's free!

Make sure to activate the proper compiler options (/Zi) in Visual Studio's property settings to produce the necessary debug information in Program Database format.

MPM Scan - Version 0.4

2009-04-23T12:58:00.012-04:00

Latest version of the software also executes in simulation mode without being tied to the PCI DAQ card. This enables it to function as a standalone desktop app in order to test certain features, portability, etc ...

Modified the interface layout to accommodate image statistic graphic view, region-of-interest selection capability, image frame resize, and multi-channel and single-channel capture modes.

Read more ...

Download latest project source code.

FCS Software

2009-01-08T14:47:00.011-05:00

An initial prototype of a multi-tau software correlator. This multi-threaded software program buffers incoming streams of photon count data from a PCI-based data acquisition board, and calculates and displays correlation results in real-time.

For now, an SX processor-based development board is used to generate steady streams of gaussian pulse train which allows the software implementation of the multi-tau algorithm to be tested.

Read more ...

Download latest project source code

Un-crashing Netburner Mod5213

2008-07-30T16:24:00.004-04:00

When programming the NetBurner Mod5213, I ran into the problem where I would get the error "Failed to Connect to Serial Port" and I could no longer download any programs (even ones that worked previously) to the board.

Apparently the code I was trying to run did something to make the 5213 very unhappy - such as a pointer to a bad location or something along those lines. So, it crashed and entered a state where it resets itself every few seconds which makes it impossible to program. A very helpful tech support person just walked me through the simple (haha) procedure to get out of this loop and back to programming. I'm posting the procedure here because it is apparently a very common problem.

-With power on and serial cable connected, Open MTTTY
-Connect to the board (File -> Connect)
-Cycle power to the board. (You should get the message "Waiting 5sec(s) to start 'A' to abort")
-Type in "A". (You should get a message with valid commands)
-To make sure it is working, load the original factory program from SerialLoad...
-Open Serial Load (Start -> Programs -> Netburner NNDK -> Serial Update Tool)
-Browse to the file Nburn -> MOD5213 -> original -> MOD5213FApp_APP.s19
-Click "Open"
-Click "Update"
-Go back to MTTTY and connect (if disconnected)
-Hit the reset button on the board. (You should get the Factory Demo program Main Menu)
-Fix whatever the heck caused this problem in the first place before trying to re-load the program

PMT Controller Update

2008-07-09T15:24:00.006-04:00

I have updated the PIC code for the PMT Controller board. I've uploaded the latest code and also a new version of the spec which reflects the recent changes. You can download these items (and any other MPM documentation) here.

Some highlights from the recent updates...

The interface between the controller and the PC has been redefined. Now whenever the controller receives any USB command from the PC, it returns a 54-byte array which contains the current status or settings of every controller register.
The controller now detects overload errors when a type 3 PMT (Hamamatsu H7422P with cooler and protection circuit) is connected to any of the ports.

The controller resets the PMT when it detects an error.

There is an error counter for each channel (which rolls over at 255).

MPM Documentation

2008-06-20T10:33:00.007-04:00

I have uploaded all of my documentation for the PMT Controller board and the USB to RS232 board. (Specs, Eagle files, and PIC code) I will keep updating this page with the most current versions of the documents.

Read more hardware/firmware docs ...

LS2K Macro - Version b1.2

2008-04-30T12:02:00.005-04:00

I went to Weill to troubleshoot the macro on the MRC-1024 system there. I found that the "ScanStart" command, which is needed to acquire an image, was causing all of the trouble. The program crashes when this command is called from within a .dll. However, the command works fine when it is called directly from the script editor. Since the .dll was necessary to create my GUI used in all the previous versions, I had to abandon the GUI idea (at least for now) and control the scope using just a Visual Basic script.

The user can specify the number of rows and columns of image tiles, percentage overlap between tiles, directory for saving scanned images, and COM port by changing the default values in the script. In a later version, I will try to include some kind of pop-op input box for these values to make it a little more user-friendly.

Sushmita has successfully used the script to scan and save a series of tiled images. It works well except that the images do not line up perfectly along one edge when "stitched" together. This could be due to backlash in the XY stage motor or perhaps an issue with the image stitching software. We are currently working on this issue.

The script (version b1.2) and instructions on how to use it can be found here.

Note: The "ScanStart" command does work from within a .dll on our Radiance system, so it is possible to use a GUI-based macro for acquiring images on our scope in Ithaca.

Scanware - Version 0.2

2008-04-28T21:25:00.009-04:00

Import and export feature for OME-XML data format has been added. Currently, only a portion of the XML schema is implemented for Scanware. The full implementation will be done a little later.

Integrated the Quinn-Curtis (QC) library. Charts, histograms and real-time graphics will be provided by the QC engine.

Read more ...

Download latest project source code.

Scanware - Version 0.1

2008-03-26T21:56:00.012-04:00

The main change has been the addition of primary MFC Automation capability which enables Scanware to become a scriptable application. The simple sequence of opening the application and clicking the SCAN button can be automated using external VBScript client code.

Read more ...

Download latest project source code.

Autocorrelator Controller - Updated UI

2008-03-17T14:01:00.013-04:00

The current version of the UI tool allows the user to continuously display the set of quick sweep samples in an oscilloscope-like fashion.

Also added a save feature to the user interface which enables data output to disk.

Read more ...

Download the latest project source code.

Overloaded Quick Sweep Function

2008-03-12T00:40:00.003-04:00

I have updated the autocorrelator class to add a quick sweep function that gives data back as it reads it.

The files are here

Also, as per Paul and my discussion this morning, the highest priority right now is to get a version of some sort that can do real time displays so we can test out the device and confirm that the rest of the hardware works. Experience using the device will probably also drive some changes to the UI.

Safer Autocorrelator

2008-03-10T17:33:00.004-04:00

I have modified the autocorrelator so that its constructor will not throw exceptions. The communication functions now can throw exceptions. It looks like Paul has the code set up to retrive and display error messages, If I am incorrect on this this someone tell me/fix it.

I couldn't figure out how upload a file to this blog, so I am linking to it on my ftp server, it is here autocorrelator.zip

Autocorrelator Controller

2008-03-07T16:27:00.006-05:00

We are currently working on a device that drives and acquires data from a pulse autocorrelator which is an optical instrument used to measure the pulsewidth of our femtosecond lasers. This device acquires a photodiode output with an ADC and drives a linear galvo via a DAC. It communicates with a PC via USB.

The device was designed by Thomas Dimiduk who has also written the communications and data processing software. Paul is working on the user interface, and I helped out with the PCB design and layout.

View the latest documentation.

Download the latest project source code (~6 MB).

-Lisa

Scanware - Version 0.0

2008-03-03T13:50:00.026-05:00

Initial prototype of the GUI application that will function as the control and data acquisition software for the next DRBIO MPM. The current version reads streaming data from an external PIC-microcontroller demo board and displays the data as RGB component images.

The latest software API documentation can be found here.

Download the latest MS VC++ project module.

-Paul

LS2KMacro – Status

2008-02-19T16:23:00.007-05:00

The macro for the MPM system is progressing, and the current version implements 4 out of the 5 original requirements.

- From the macro GUI, the user can enter the number of columns (X direction) and rows (Y direction) to be included in the scan.

- An input box allows the user to define the degree of overlap between the frames.

- The scan can be interrupted in mid-operation by clicking the “Stop” button. Then, the user can either continue the scan from the current position by clicking the “Resume” button, or the “Start” button can be used to start a new scan from the beginning. If the user-defined settings such as X and Y frames or overlap are changed, these new settings will be used the next time Start is pressed.

- A check-box is used to provide the option of homing back to the starting position at the end of the run.

This version of the code has been tested on our system using LaserSharp2000. The features described above worked successfully, and we were able to view the images scanned by the MPM after each movement of the XY stage to the next frame.

This macro code and installation instructions can be found at http://dev.drbio.cornell.edu/lt222/LS2Kmacro/downloads.html.
Look for files under the heading "a.92". Please note that some features of the GUI are for development purposes only (such as the listbox and cheesy graphic), and this will not be the final format of the interface. Any comments/suggestions about features wanted in the final format would definitely be appreciated!

As for the next step… I am currently working on automatically saving the image files directly from the macro. I am also working on a method for taking z-stacks of selected frames. I have been developing one possible method for selecting the frames graphically. This involves overlaying a grid (each square represents one frame) on an image of the entire field of view, and the user can click on each frame they want a z-stack of. Another possible method would be selecting the frames numerically. I am also getting input from MPM users on methods they might like. (Again, any comments would be appreciated.) Another feature I will try to add in future versions is the option to move the stage to a user-selected position at the end of the scan.

-Lisa

LS2KMacro - First Test

2008-01-22T10:11:00.003-05:00

The BioRad Radiance system is supplied with either Marzhauser or Ludl motorized XY stage. So it seems that it works with either one or the other out of the box. We'll need our macro to communicate with a different stage controller (ASI) with its own command set and firmware altogether. As a first step, we need to validate a basic requirement; make sure the LS2K macro can control the XY stage via RS232. A VB macro has been created to do just that. If everything works, it will display a simple user interface and the user should be able to perform basic stage movements with the GUI. The following link has the ActiveX DLL component and other necessary information to conduct the test. Look for version a1.0

http://dev.drbio.cornell.edu/pl47/downloads.html

-Paul

ActiveX DLL in VB6.0

2008-01-21T17:01:00.001-05:00

The following link is a quick tutorial that covers how to create a very basic ActiveX DLL in Visual Basic 6.0.
http://www.xtremevbtalk.com/showthread.php?t=7290

This next link gives a much more involved tutorial. It's a bit more complicated to follow, but it can also be a useful tool.
http://msdn2.microsoft.com/en-us/library/aa229332%28VS.60%29.aspx

We found these tutorials to be helpful when learning how to create DLLs for a macro used to extend software capabilities of the BioRad LaserSharp2000.

-Lisa Toth
(Research Support Specialist)

First DRBIO Blog Entry

2008-01-19T15:39:00.000-05:00

Hello. I'm Paul Lee and I'm one of the staff members working at DRBIO (Developmental Resource for Biophysical Imaging Opto-Electronics) Research. I created this blog as an experiment for information dissemination on MPM-related software and hardware tasks. This forum seems like an efficient way to organize thoughts and ideas chronologically, while fostering feedback from interested parties. Hopefully, it will make the MPM development process a bit more transparent.

-P