jClamp Features

Copyright 1996-2018

jClamp for Windows (v. 30.5) 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.
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New Feature Update
   -10/26/18 Version 30.5.0
   Update Utility can now deliver support file updates other than jClamp executable updates. Automatic restart of jClamp after these support updates.
   Microsoft has change its msi installer so that previous versions of jClamp are not automatically uninstalled when you do a web update. Go to the web and download jc_updat.exe <here> to the Desktop then drag to the jClamp directory to do an automatic uninstall before installing jClamp ver. 30.3.0 via jClamp update. Alternatively, you can manually uninstall an earlier version, and then install 30.3.0 with future installations working as before.
   NI USB-6218 support, multiplexed and no synchronous digital output. Select ni_usbx in ini file.
   Bug fixes.

-10/12/18 Version 30.1.0
    New shortcut bar allows bypass of User Account Control popups.

-10/5/18 Version 30.0.0
    USB3 camera support. E.g. Basler acA640-750um can capture small regions of interest at about 3000 FPS. About $400.
    Enhancements and bug fixes.

   -8/21/18 Version 29.5.3 (quickie update)
    Internal jClamp difference equation math model can be set to oversample in Model Cell window to give more precise results. Oversample to 1, 0.1, or 0.01 us, with relative increase in sample size (so some protocols can be too big to run). Applies to CC and protocols. Down sampled back to original clock for analysis.

   -8/16/18 Version 29.5.2 (quickie update)
    Added holding potential temporary jump in CC Cs software stray cap comp auto fitting routine. Useful to jump to a linear capacitance region where stray cap comp is valid in whole cell mode.
    ABF search added list of all parameter files used under selected path. Click on parameter to open abf files that used parameter.
    IniEditor missing tabs fixed.

-8/1/18 Version 29.5
CC auto save (set in ini; toggle in CC, shift right click over CC Save) - turns on CC Save when CC is turned on
ABF search for associated video files with export to new directory; rate and frame number info.
Phantom camera video analysis updated. Subpixel shape tracking for jClamp collected Phantom camera movies. Select image fitting setting saved with abf and exported to Matlab.
ini file saved with abf file. Loadable from Data Load window (select file type as abf[ini]). Opened in IniEditor and saved in data directory. Each ini check resets data load file type to abf.

-6/30/18 Version 29.4
Fastlook! and Look32X update
export selected abf files to new directory in ABF search

-6/22/18 Version 29.0
Digidata 1550A, B0 support
fast fitting software-based stray capacitance compensation with pass through to Multiclamp Commander and EPC10
auto fitting and export
user enhancements/bug fixes

-4/22/17 Version 28.0
Vision Research Phantom High Speed Video Camera support
HEKA EPC10 USB amplifier support - up to 4 amplifiers (if less than 4 amplifiers, supplement with non-EPC amplifiers)
Molecular Devices DigiData 1550 jitter fix confirmed
Security changes; some old license files may only work for versions prior to v.28.0; you must request updated license if needed
chirp-based stray capacitance cancellation
user enhancements/bug fixes

Calibration of your system is crucial to measure cell capacitance. A new chirp method is used to calibrate the system
Command window enhancements, resizing and copying among partitions.
user enhancements/ bug fixes.

auto cursor increment with iv analysis
user enhancements/ bug fixes
simultaneous Rs and Cm view in CC to balance stray capacitance in while cell mode
new Cm calibration routine and files. Calibration resister measured automatically. Old calibration files still work.

Ability to search ABF files in multiple subdirectories for particular characteristics of the command protocol or clamp characteristics. Shift right click on displayed file list to copy list to clipboard, e.g. to paste into Excel. Copy all listed files to a new directory to do group file analysis, e.g., to analyze all data collected with a particular protocol file. Double click on a file to plot data in Analysis window.
Command protocol window shows actual max/min, including 2 sine stimuli. During build, if magnitude is over board settings then a notification is given. If such a protocol is run a choice is given to cancel or proceed.
Parameter directory fixed at jClamp diretory subfolder "/param", with subfolders below automatically entered into search path from RPD and scripts.
Crash detection implemented in jClamp registry key. Logs crashes for debugging purposes.
·         -12/30/14
·         Automation links remain in effect when exiting Analysis mode. This allows quick re-entry to analysis mode rather than checking for connections each time. No need to double click on the SigmaPlot, Matlab, Excel or Origin icons in Analysis mode. If programs are available (but need to be set to check for [in in file]) then icons will display and drag/drop icons to transfer data will be immediately available.
·         In order to use SigmaPlot jClamp templates, available in jClamp SigmaPlot directory, you must load them into the template.jnt file according to Sigmaplot instructions. You can add templates for access in jClamp by creating your own in SigmaPlot and putting the names of the template in the jClamp/SigmaPlot directory (e.g., make a file name "my_new_template.jnt" in the directory -- it can be an empty file, only the file name is necessary and must match the template name "my_new_template" in the SigmaPlot template.jnt file. Check that the new template is available in sigmaplot. It is required that you reload SigmaPlot to install new templates that are added to template.jnt.
·         Sigmaplot transfers will now increment notebook numbers so that now saving with new names is not required between jClamp->SigmaPlot transfers. JClamp data file names are inserted in notebook sections.
·         All transfers of data to other program via automation will  leave the automation program files open after jClamp closes. You can continue work on the data in those programs (SigmaPlot, Matlab, Excel or Origin) and save what you like. Matlab will ask before closing, Xcel will ask to save data before closing. SigmaPlot will not close. Origin?
·         Selection of DD1550 board sets clock increment to 2 us because that is required by MD. There is still a jitter that I detect that MD cannot recapitulate. I think it is present not just in jClamp but also in Clampex. I will fix when they acknowledge and fix. In order to use MD (Axon) boards you will need to copy some files to the jClamp32 directory. The required files change, so email me for information.
·         FFT and PSD analysis bugs fixed.
·         A Matlab script to do PSD analysis on jClamp files can be provided.
·         -12/15/14
·         JClamp now supports Molecular Devices DigiData 1550 (there is an intermittent one point jitter in their driver so that high frequency Cm measures are not stable). Molecular Devices (MD) is working to fix the jitter, and I will update when this happens. Lower frequency Cm measures are less susceptible to the jitter. Update (SEE ABOVE): MD has just released a new version of pClamp (v. which apparently fixes the jitter issue in pClamp (Clampex). However, clock rates are limited to multiples of 2us. Thus, older versions of Clampex collected data that had the potential for inaccurate timing when using the 1550. jClamp does not currenly support the 2us increment limitataion on sampling, and, in any case, the new drivers still produce jitter in jClamp even at 2us sampling. I'm trying to figure this out. Unfortunately, I do not recommed using the 1550 with jClamp at this time.
·         MultiClamp Commander Telegraphs are now supported internal to jClamp – no need to run jc_Client applications anymore. Set MultiClamp on in ini file History tab. Provide paths to MultiClamp servers (MC700.exe and MC700B.exe) in the ini file and select the associated check box to run automatically. Only one Multiclamp (700A or 700B is supported).
·         Multiclamp mode can automatically be controlled by digital out 3 in a protocol file. Multiclamp Commander must be set to “ext” control. This means that voltage clamp and current clamp can be switched real time within partitions of a command episode (protocol command type must be set to voltage clamp). Only channel 0 in/out command protocol should be used. Other channel inputs can be sampled as usual.
·         Drop down box in Data Load Window allows quick selections of previously viewed data directories.
·         Previously channel protocol holding potentials were set prior to running the protocol (500 ms plus a computer dependent variable time preceded the protocol command). This eliminated a transient in the protocol response if the CC holding potential were different. Since you should be aware of mismatch in CC hold and protocol hold, this feature is now removed. Now, you will see a transient current response at the onset if CC hold and protocol hold do not agree. You must make sure that CC holding potentials are the same as the protocol holding potentials for all channels that are active.
·        Prior Update:  
·        Midnight issue fixed. At midnight a new directory will be made for data collections. If CC save is on it will turn off and restart for saving in new directory.
·        Inter-episode times are now saved with data file. View by moving mouse cursor over inter episode time in command protocol window in Analysis mode.
·        Prior Update:
·        Sister parameter files - individual files can be linked to follow each other (simple alternative to script files). For example, jclamp.prm, test.prm, test1.prm, and test2.prm can be run sequentially by renaming first file to jclamp[test.test1.test2].prm.
·        New box in Parameter load window lists files by date or by today's use. This supplements typing names which lists by matching.
·        ABF fileload window info reports if math model was used. If Matlab model was used script is appended to abf file and then shift right click on filename opens script file in text box.
·        Cm calibration file is correctly listed when mouse is over calibration button in Analysis window. The file has always been appended to abf files for Cm corrections.
·        Works in Win 8. Set run as administrator in shortcut.
·        And, of course, bug fixes.
·        Full installation to use 7Zip compression for quickie updates. Bugs fixed as well.
·        Updated MD in-cell stray capacitance compensation with software assistance, including automatic compensation – see Cm Analysis in Help file.
·        Digital trigger now has minimal delay between triggering and data collection, except for protocols with P/N, prepulse or CC inter use.
·        Cs stray capacitance compensation prior to cell pop-in disabled. Replaced by robust  in-cell stray capacitance compensation using MD (multi-dual) sinusoidal stimulation (see help file).
·        Molecular Devices releases new Axoscope (pClamp) with new DLL to fix spurious voltage output, and allow digital output during 4 DAC output. jClamp v22.7.0 and above uses this fix.
·         Support for the Tecella Pico USB patch clamp amplifier (www.tecella.com). Up to four units running simultaneously.
·      Support for 4 DAC outputs for those boards that have four DACS, including the Axon DigiData 1440A, IOTech Personal Daq, and soon the CED Power.
·          The previous full version was the last one that supports only 2 DAC channels.  Future versions (coming soon) will support 4 DAC outputs for those boards that have four DACS, including the Axon DigiData 1440A, IOTech Personal Daq, and CED Power.
·         jClamp will now automatically startup with the last ini file selected in the Identity window. An edited shortcut will override last selection if different. Remember, to make an edited shortcut linking directly to your ini file, edit a newly created shortcut Target property by placing your ini file (e.g., my_ini_file.ini) at the end of the target command with a space in between the two. To access the properties of a desktop shortcut, right click and select properties.
·         Support for both Axon Multiclamp 700A and 700B  telegraphs. Previous version only supported the 700B. See the jClamp help file under Telegraph.
·         Support for new board, NI USB X Series. Amazing! 1 megaHz 16 bit sampling on all 8 channels without multiplexing. Synchronous digital output.  About $3K. Could not ask for more. The new NI-DAQmx 9.3 drivers  need to be installed.  Visit NI at http://joule.ni.com/nidu/cds/view/p/id/2337/lang/en.
·         User info (License owner, board, operating system, disk size and memory) collected when check for updates occurs.  Useful for me to identify user issues and aid in debugging.
·         Automatic or manual check for new version of jClamp on the web – set choice in ini file under Script Tab.
·         Impedance analysis with Nyquist/Bode Plots and model fitting
·         Additional script commands to control CC window parameters
jClamp Features
·         Vista and Win7 users must disable User Control Account in Users Dialogue!
·         In-cell stray capacitance compensation for Cm measures.
·         Digital flip-flop overrides partition digital out in command protocol.
·         Look32X! video capture with cameras and devices with DirectShow or VFW drivers. Synchronized video capture with electrophysiological data (as best as Windows will allow! TIFF and other image file support.).
·         FastLook! -- Andor (www.andor.com) camera support and Prosilica Gige (www.prosilica.com) vision camera support. Link video frame capture to patch clamp data collection. Synchronized data for each frame. Export automatically to ImageJ for video analysis. Combined with jClamp or standalone program available.
·         CellSeeker and MagicSeal coming soon!
·         Automatic offset current cancellation
·         User control over audio feedback during seal formation.
·         Enhanced P/N subtraction.
·         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
·         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.
·         Detached Telegraph window with only the enabled channels (from 1-4 for each of the two supported amplifiers) displayed.
·         Vista and Win7 support
·         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
·  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.
·  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!
·   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.
·         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.