jClamp

: jClamp for Windows (v. 18.8.0) is a user-friendly whole-cell voltage clamp data acquisition program which features real time monitoring of cell and voltage clamp characteristics. At all times the patch clamper can determine cell status. Data collection is initiated through a rapid parameter directory (RPD) which maintains a list of 18 parameter filenames or script filenames. Either a key press or mouse click begins the predefined voltage or current delivery protocols. Scripts are text files which allow groups of parameter files to be called and run. Most tasks are automated. Some data analysis is available. In addition, automation links with MATLAB, Excel, SigmaPlot and Origin are available

jClamp is now FREE to use with the Axon 1200A & 1200B and the old Labmaster DMA!!! Remember the free license is only available when the ini file is set to use the Labmaster board or axdd1200 board (under gain tab). Set the proper address for the Labmaster! The Labmaster board is controlled exclusively through Port I/O witht the jClamp VXD or SYS driver. The only differences with the hardware setup required by pClamp is that the ports A0-A7 should all be configured for output. A7 is scope trigger. See the hardware manusal. B0 is trigger input. C channels are not used. 2-sine protocols are supported. Win 2000/XP Pro performance is superior. The Axon 1200 board needs the DriverLinx installation (NT version for Win2000 and above). Axon supplies the drivers. Email me if you have a problem getting them. Axoscope 9.0.2.05 supports the board, so you must use that program to verify that everything is working before using jClamp. Normally, if there is no hardware license the registration window will appear, indicating that the license is software only or that so many days are left in the hardware fulldemo license. For the free labmaster or Axon 1220 support, there is no license, so the register window will open. If you want to bypass that window you may create a shortcut on the Windows desktop to jclamp32.exe, as you would do for any other program. The shortcut made during jClamp installation cannot be edited, you need to create an editable one by going to the jClamp directory and right ckick over the jClamp32.exe file and send shortcut to the desktop. Then you can edit the new shortcut. In the properties window, target line, you should append the word "skip_reg". For example, <"C:\Program Files\jclamp32\JCLAMP32.EXE" skip_reg> is taken from the target line of a shortcut. It will run jclamp but not display the registration window. You could also specify a particular ini file other than the default jclamp32.ini by doing the following. <"C:\Program Files\jclamp32\JCLAMP32.EXE" my_ini_file.ini skip_reg>. Note there is a space after the executable name and between the ini filename and "skip_reg". See supported hardware for more information Email me so I can keep track of users.

Nanion Port-o-Patch support is here!

You can see supported hardware info (here).

You can see the detrending for CM analysis technical note (here).

New Feature Update

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· Vista users must disable User Control Account in Users Dialogue!

· CellSeeker and MagicSeal coming soon!

· Automatic offset current cancellation

· User control over audio feedback during seal formation.

· Enhanced P/N subtraction.

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· Switch polarity for whole cell or inverted patch in CC window.

· Disable dual patch mode in CC for stimulation with channel 0 or 1 D/A while recording from channel 0

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· Removal of stray capacitance effects on calibration and during cell recording for Cm analysis

· Plots of Real and Imaginary components of raw currents

· Simple way to set angle of dRs/dY-90 or angle of dC/dY in Phase detector Admitance Window, and angle will be used by single sine protocol to get Magnitude at 0 and 90 degree phase for C and R analysis. Note that using Rs compensation (or an Rs dither) and C compensation (or a C dither) for dithering is a poor method for dithering actual Rm and Cm if Rm is not much greater than Rs, or if Rm or Cm changes substantially during your experimental measurements -- the limitations of single sine analysis

· Non-harmoninc two sine stimuli to avoid nonlinear distortion interference with Cm measures.

· Free support for the Axon 1200A and B boards that Axon no longer supports with their new software! See supported hardware for more information.

· Support for the IOtech PersonalDaq. It is a great board (~ $1,400) with many capabilities, close to the Axon 1440 series.

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· Detached Telegraph window with only the enabled channels (from 1-4 for each of the two supported amplifiers) displayed.

· Vista support (I think!)

· Detached PDF Help file in addtion to Windows Help file. You can search and print out the help file.

· Separate Audio program (jc_audio.exe) for recording/playing MS wav audio files, which can be played during script execution now, since Windows Vista does not include one.

· Multiple instances of jClamp can be run, each controlling a different A/D D/A board! Or use another instance to analyze data while the first instance is actively collecting data.

· Frequency analysis can successfully monitor bilayer prep capacitance, making jClamp a good choice for these types of studies

· Cell Censor window provides full cell parameter analysis either in Time or Frequency domain

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Axon Multiclamp telegraph support.

User selectable channel input for telegraphs.

Real time, scalable plotting of Cm or Im vs time or voltage collected with protocols.

Support for Axon 1440 series!

Support for National Instruments M series boards. NI 6251-USB and NI PCI-6221, in particular.

NI boards that use Ni-daqmx driver (M series and also the PCI-6052E) and Axon's 1320 and 1440 series now can have dual analog output and up to 8 input channels.

The NI PCI-6221 board is used by Neobiosystems to control their ( PatchMAX 100A ) and jClamp will work with their system to provide user friendly patch clamp and two electrode voltage clamp solutions.

User choice of Dual frequency Cm calulation from f1, f2, or aveage of both.

Phase Sensitive Detector (PSD) exposed for phase analysis.

Automatic fusion event analysis.

Easy capacitance measures – new method based on actual angle of dY/dCm – perfect at last!!.

Average after all episodes are run or average each episode before continuing to the next episode..

Smart averaging – only average as many runs as required to reach a desired signal to noise ratio!.

More flexible delivery of frequency stimuli.

Axon 1322A support.

Storage view in Analysis mode – view two data file plots simultaneously (previously opened and current) .

Independent analysis and data collection CM calibrations file loading.

Streamlined generation of command protocols from ABF data files .

User choice of detrending of raw data prior to CM analysis (Technical Note released) .

NI PCI-MIO-16E-1, NI PCI-MIO-16E-4 support.

Fitting with user supplied equations.

Now measure capacitance with either 2-Sine analysis or Phase tracking.

Very detailed information for all files in data directory in data load window when info button is pressed.

IV plot window calculates reversal potential, and slope resistance; multiple I-v plots for comparison.

Quick notes window allows button click insertion of pre assembled, often used notes into the log file.

Conditional scripting with parameters from Cell Censor. For example, wait for membrane resistance to reach a certain value before running a protocol.

DCM files are only saved when enabled in ini file under History tab.

CED Power 1401 support. Four DAC outputs; control four patch clamp amplifiers. Channel watch channels moved from 2-5 to 4-7 for all boards. Shell out (from Data Load window) to Adobe Acrobat or reader to look at lab notebooks. I suggest that you scan in your hand written notebooks as an image and place a PDF conversion into each day's data directory for viewing. NT and 2000 support for Labmaster DMA and Daqp 308 boards. jClamp for the old Labmaster DMA board is FREE!!! No license needed. Great for student labs!!!! Break out those old boards and put them in some new, fast and cheap computers.

jClamp for the Labmaster DMA is free -- no license required. Remember the free license is only available when the ini file is set to use the Labmaster board (under gain tab). Set the proper address! The Labmaster board is controlled exclusively through Port I/O witht the jClamp VXD or SYS driver. The only differences with the hardware setup required by pClamp is that the ports A0-A7 should all be configured for output. A7 is scope trigger. See the hardware manusal. B0 is trigger input. C channels are not used. Cm tracking and gap-free are functional only in Win 95/98, althought 2-sine command protocols are supported. Win 2000 performance is superior. Normally, if there is no hardware license the registration window will appear, indicating that the license is software only or that so many days are left in the hardware fulldemo license. For the free labmaster support, there is no license, so the register window will open. If you want to bypass that window you may create a shortcut on the Windows desktop to jclamp32.exe, as you would do for any other program. In the properties window, target line, you should append the word "skip_reg". For example, <"C:\Program Files\jclamp32\JCLAMP32.EXE" skip_reg> is taken from the target line of a shortcut. It will run jclamp but not display the registration window. You could also specify a particular ini file other than the default jclamp32.ini by doing the following. <"C:\Program Files\jclamp32\JCLAMP32.EXE" my_ini_file.ini skip_reg>. Note there is a space after the executable name and between the ini filename and "skip_reg".

Multiple stopwatches.

Streaming video capture and playback; record video during data collections; control through script or via Look! video window. Screen shots available from scripts.

CM calibration changed to provide more resolutions. accalib.prm and accalibi.prm are revised. Please recalibrate to use extra resolutions. Remember to check proper function with electrical model!!!!!

Channel watch is functional (if enabled) even when CC is not running.

Conditional scripting. Continue scripting after switch from/to current/voltage mode or based on values obtained from analog Channel Watch (e.g. based on temperature change reading).

Ability to transfer voltage clamp holding current to current clamp upon mode switch. Also, current clamp membrane potential to voltage clamp.

Ability to set all partition start voltages/currents to holding level in Command Build Utility. Useful when passing hold from Cell Censor to protocol.

Better memory management in Win 98. IniEditor can now be opened from within jClamp without "out of memory" error. Tested with 128 Meg memory system.

Automation link with SigmaPlot 2000, Excel 9, MATLAB 5.3 and Origin 6. Rapid data transfer and plot generation. May work with some earlier versions. Enable use for each program seperately in jclamp ini file. Scripting of application commands in jClamp analysis scripts.

Two sine FFT based CM tracking now supported under current clamp.

Ability to use data file (abf) traces as commands in Command Build utility. Automatic generation of command parameter files from abf data files. For example, immediately stimulate cells in current clamp with currents obtained under voltage clamp. Also, FFT can now be computed on any portion of data trace with automatic zero padding.

Support for the National Instruments PCI-MIO-16EX-10 (10 usec) and PCI-6052E (3 usec) boards, 16 bit A/D, D/A-- boards with breakout about $2K.

Support for the IOtech daq2000 PCI board. 16 bit A/D, D/A @ 100kHz -- board is $500! Cabling and breakout extra. Important -- contact me before getting one (there is a glitch on analog out).

High time and magnitude resolution capacitance measures during episodic protocols! Measure capacitance, Rs, Rm simultaneous with your favorite step, ramp or AC protocols. Automatic analysis. Episode length up to 1 million pts for Axon boards and IOtech daq2000 -- measure voltage induced capacitance changes up to 10 seconds per episode (@ 10 us clock)! 10 million pts for National Instruments boards!

jClamp Features

Real time monitoring of cell and clamp characteristics in Cell Censor Window. Full control over two patch clamps. Channel 0/0 [A/D- D/A ](patch clamp #1), channel 1/1 [A/D - D/A] (patch clamp #2), both channels or junctional coupling possible. Pseudo-simultaneous measures under current and voltage clamp on channel 0 and 1 in Cell Censor. Automatic pulse polarity flip-flop for charge buildup control.
Four additional channels can sample peripherals (e.g., pressure monitor) at user selected rates
Works with either the DigiData 1200, 1200A or 1320 series boards from Axon Instruments, Labmaster DMA, IOtech daq2000, National Instruments PCI-MIO-16EX-10 and PCI-6052E boards or Quatech DAQP-308 PCMCIA -- have Lap can Clamp!

I suggest a Hauppauge video capture card - you can get them without the TV tuner for less than $100.

Connect to Hauppauge to check out the Hauppauge WinTV PCI video boards

Connect to NI to check out the PCI-MIO-16XE-10 board and connection hardware

Connect to NI to check out the PCI-6052E board and connection hardware

Connect to Iotech to check out the daq2000 board and connection hardware

Connect to Axon Instruments to check out the 1320 series systems

Connect to Quatech to check out the Daq-308 PCMCIA card and connection hardware

Connect to CED to check out the CED Power 1401

Connect to Scientific Solutions to check out the new Labmaster Boards and connection hardware

Convert digital outputs to analog outputs with the optional DAX (D/A eXtra) hardware add-on. Control up to four more amplifiers. Monitor seal formation, set holding potentials, monitors cell characteristics, synchronous episodic delivery.

Four channel graphical history display of selectable cell and clamp characteristics - time window user adjustable.
Graphically view seal formation with frequency varying audio cues.
Customizable initialization settings for individual users - including graphic ID in Cell Censor window. Separate initialization file editor.
Automatic data directory naming, file naming and saving.
Powerful graphical voltage/current protocol build utility. Episode length up to 10 million for National Instruments boards, 1 million pts for Axon boards and IOtech daq2000, 128k pts for Labmaster and DAQP-308. Step, ramp and AC stimuli (one, two or three sine; chirp). Dual command protocols support simultaneous current and/or voltage clamp. Gap free collection is supported. Full command waveform scaleable based on user scale factor set in INI file. For example, with a button press increase or decrease the wave form magnitude by a factor of 2 about the holding level. Additionally, toggleable timing increments by a factor of 2. Automatic saving of individual runs during averaging.
Protocols can be run at the press of a key or click of a button. External file based user stimulus incorporation. Arbitrary number of input channels and order of input channels in parameter files. Analog output is through channel 0 or channel 1, or both simultaneously. Each parameter file contains information for separate and distinct command waveforms for each output channel. Random episode delivery; auto supplemental A/D gain (1-8X) {Axon 1200, DAQP-308 and daq2000 boards}; dual telegraph inputs to control gain and clamp type, and monitor capacitance and filter frequency.
Digital output during, before, after or synchronous (depends on board) with analog output.
TTL or key triggerable starts - full run or individual episodes.
Text, audio and video (time lapse grabs, or linked to data collections[after each average, or episode]) clips can be saved, and easily retrieved and played during analysis. Any Windows compatible cards with wav audio drivers and video for Windows drivers will work.
Script files can run individual protocols or loops can be programmed; wait periods are allowed between protocols and during these periods cell and clamp characteristics are continuously monitored and saved to disk. Control holding potentials (main board and DAX); output serial port commands, e.g. to control external hardware [GPIB under construction]; set digital out ports; trigger video capture or time lapse capture.
Scripts can be automatically canceled if one or more particular cell or clamp characteristic crosses a predefined threshold; e.g., if resting membrane resistance (Rm) drops below 50 Mohm or if electrode resistance rises higher than 40 Mohm.
Analysis features are smooth and graphical. Axes or scale bars. User text on plot. Episode math, file math, fitting of exponentials, Boltzmanns, FFT. Residual series resistance correction, cursor based analysis, IV plots, togglable leakage subtraction (view raw or subtracted traces), x-axis data shifts. Exporting of data to abf, atf, ascii, or matlab. Copy plots to clipboard for paste in word processors. Trace comparator - combine traces from Analysis window into new window for comparison across files.
Data file loading is enhanced by the ability to view key items in the file before loading; e.g. data owner, cell and clamp characteristics immediately prior to data collection, parameter file name, sampling clock, number of channels etc.
All data collected can be summarized in printed form. Each protocol and associated data traces are printed along with key protocol parameter information - four data files per page. All cell and clamp characteristics for each cell studied are plotted versus time.
Data files can be selected by parameter filename and printed or plotted on screen (plots have selectable interplot periods and a pause feature).
Each data file has appended the parameter file in ASCII format, allowing the display of all information in the build utility during data loading. Key ASCII information can be searched for and files save to a new directory for group analysis.
Logging implemented. Recall and play (abf, cc, cm, not [audio, video, text, cc clip] ) files from log window with button click. Search logs for information. Show all logs on disk. Edit them. Log is run from Main menu bar in jClamp (when in Analysis mode), or can be run as an independent program (jc_log.exe).
Capacitance tracking allows monitoring of cell characteristics using two sine FFT based analysis with analog and/or digital stimulation (prepulse, incrementing pulse, ramp) at 2.5 or 5ms resolution and noise of 10fF (model cell with 200 MHz Pentium). Additionally, capacitance, Rs, Rm can be measured simultaneously with your favorite step, ramp or AC protocols. Automatic analysis. Very powerful feature!
Analysis scripts. (under construction)
Binary save of Cell Censor and CM tracking data files. Faster save and load, and smaller size. Ability to save in ASCII format set in INI file.
"Screen Shots" to save jClamp window arrangements for instant retrieval; Collapsible Cell Censor window. Sizable plotting window during data collection (drag to size). Unobtrusive RPD window, updated searchable help file (including help on the new features). Screen shots can be loaded at the command line in a shortcut -- "jClamp.exe myinifile.ini collect.scn" will bypass the Identity login form and load the saved sreen format.

jClamp32 - $1,200 for educational institutions. Contact me for non-ed costs. As always, free updates. Please cite jClamp in your published manuscripts.

Files may be downloaded for a trial examination.

email me for a username and password; please include your affiliation, operating system and hardware.

I suggest a fast computer (>1GHz), at least 512 Meg memory, and fast video! jClamp is a large program. It works best in Win NT, 2000, XP, or Vista - for those boards which can work in these environments. Cm tracking with the Axon 1200 board has problems in Win NT if run from Cell Censor but not within command protocols. All will work in W95/98, however.

	Name	Last Modified	Size	Description
	jClamp Help file	10-May-2008	1.8M	jClamp Help file (jclamp32.chm); to view you may need to unblock in the security tab of the file properties
	INSTALL.TXT	1-Jan-2008	5K	install information
	getting_started.htm	1-Jan-2008	1K	Getting started and Labmaster DMA support
	jc18800.exe	24-Sep-2009	22M	New 32 bit (v 18.8.0) version setup files [make sure to check below for an updated jc_exe.exe]. For the Axon 1320 boards their new driver is necessary (Check to see that channels 8-15 are correctly working in Axoscope, I have had a problem but you may not; get the Axoscope update at http://www.axon.com/cn_Axoscope_Update.html[remember to turn off/on the 1322 and reboot]). The new jClamp version will work in Win Vista/XP/NT/2000/Me and /98 (I hope with no problems!!!). Versions above 6 do not supply any board drivers; they should be installed from the board manufacturer. In particular, the Axon 1200 drivers (DrvLnx95.exe and DrvLnxNT.exe) and the 1440/1320 series drivers should be installed before jClamp. jClamp will not overwrite them. See below for a list of files that should be deleted before installing the 1200 drivers, so that the Axon versions are installed. For the 1320 series, the driver (AxDD132x.dll [no more Axoutils32.dll to worry about]) found under the Axon directory should be copied into the jclamp32 directory for the boards to work with jClamp. See above for features. Per-machine license required. Software demo license included. Time-limited hardware license see below. Read install info.
	jc_exe.exe	Whenever	1.1M	New 32 bit executable (do not use with previous versions before the latest posted full install - look here for newer executables - the link will be empty if no update exists). Place in jclamp32 directory, double-click to extract jclamp32.exe and select overwite to replace the old version. No need for full install if posted full version was installed.
	ax_driv.TXT	23-Oct-2000	1K	installed Axon driver files
	fulldemo.lic	Monday	1K	30 day hardware license for evaluation (jClamp version 16.0 and above). Rename to jclamp32.lic and replace the software-only license file in the jclamp32 directory.
	detrending	14 Feb 2003	500K	Technical Note on detrending data before FFTing for CM analysis. User can now choose whether to use detrending.

Connect to Axon Instruments to download Axoscope and the Digidata drivers for Win95/98 and WinNT

Copyright © 1996-2009 J. Santos-Sacchi [SciSoft]
Last modified: Aug 25, 2009