Nadim · Golowasch · Bucher

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Software

A collection of Spike2 Scripts for analysis of electrophysiological data, mostly written by Dirk Bucher. Last update: 08/15/14+

This is a collection of Spike2 scripts written in the years since 2002, mostly by Dirk Bucher. This means that they were written in Spike2 versions 3-8. Most of the older scripts have been tested to work in newer versions, and usually CED makes sure there are no problems. However, scripts are not necessarily backward compatible. Feel free to contact Dirk Bucher if there are problems. The quality of the scripts ranges from “fast hack” to well designed and user-friendly. In addition, some are designed for broad use, while others are fairly specific for tasks that came up in the Marder and Bucher (and other) labs over the years. In general, apart from things like view manipulations that could be useful for anyone, there is a heavy bias toward analysis of rhythmic patterns and spike timing. General use scripts are listed in bold below. Scripts written by Dirk Bucher are in most cases designed to be run from the script bar and close automatically. If you prefer running them from the file view and keeping them open, “out code” the FrontView/FileClose lines at the end. Most scripts accessing time view files automatically operate in the time range between Cursor (1) and Cursor (2). If those are missing or in the wrong order, you’ll be asked if you want to analyze the entire time range instead. With most scripts that output numerical values, results are written into the log window and can then be saved as text files. Annotations are spotty. All scripts have a header with instructions/descriptions. However, the code itself is only annotated in some cases.

Descriptions of the scripts are shown below. You can either download them one by one or you can get all scripts in a fairly small zip file here (version 1604). Also includes a word file with script descriptions.

Click script name to view code in new window, or right-click to "save link as".

Burst Analysis

1spkMkburst - Creates burst markers at single events, allows using burst and phase analysis scripts when one of the neurons only spikes once per cycle. Dirk Bucher (2007). General Use

batchbfast - Does fast burst analysis for one channel in a sequence of files. Only returns means and SDs for burst duration and cycle periods. Intended for analysis of long-term recordings. Dirk Bucher (2002). General Use

batchburst - Does full burst analysis for one channel in a sequence of files. Intended for analysis of long-term recordings. Dirk Bucher (2002). General Use

burststat - Does single channel analysis of discrete bursts. Dirk Bucher (2003). General Use

gastBin - Analyzes burst parameters of a pyloric neuron over the normalized gastric mill cycle (in gastric cycle bins). Written for the Nusbaum lab to analyze gastro-pyloric interactions in the STG. Dirk Bucher (2015). Specialized

gastropyloric - Does burst analysis of a fast rhythmic signal with respect to a slow rhythmic signal, written for STG data to analyze when each pyloric burst happens in the gastric phase. Dirk Bucher (2005). Specialized

gpPhase - Does burst and phase analysis of a pyloric reference neuron and an additional pyloric (follower) neuron with respect to the phase of a gastric reference neuron. Written for the Blitz lab to analyze gastro-pyloric interactions in the STG. Dirk Bucher (2013). Specialized

missburst - Checks the regularity of alternation of two bursting neurons. Returns normal burst statistics for a reference channel and number of bursts of a second channel in each reference cycle. Quick way to check how much cycle skipping occurs. Dirk Bucher (2012). Fast Hack

mkbursts - Does burst detection from spike events. Creates a marker channel that holds burst starts and ends. Dirk Bucher (2002). General Use

nSpks - Plots the number of spikes per burst into a RealMark channel. Can be used as fast check for burst variability. Dirk Bucher (2012). General Use

periodcount - Counts the number of pyloric cycles (with fraction) within each gastric cycle. Dirk Bucher (2005). Specialized

phaseburst - Analyzes rhythmic bursting in 2-3 neurons fairly completely (in phase and time, and with optional spike analysis). Dirk Bucher (2002). General Use

PRC - Does phase response curve analysis. Dirk Bucher (2003). Fast Hack

pyloricBmk - Detects PD, LP and PY spikes and bursts if good enough for simple thresholding (faster than doing it one by one). Dirk Bucher (2005). Specialized

pyloricPhase - Customized version of "phaseburst" for analysis of pyloric rhythms from extracellular recordings. Dirk Bucher (2003). Specialized

pylPhConsec - Pyloric phase analysis from consecutive files toanalyze long-term recordings. Dirk Bucher (2005). Specialized

The_Crab_Analyzer - Does Spike detection , burst detection, and phase analysis to quantify pyloric and gastric rhythms all in one go. Wolfgang Stein (2009). Specialized

trigBurst - Does analysis of repetitive episodes of bursting. Dirk Bucher (2005). General Use

 

Channel Editing

AddChan - Generates an event channel that holds events of two input event channels. Dirk Bucher (2002). General Use

artiCut - Cuts out stimulus artifacts from a waveform channel and replaces them with a linear interpolation. Useful for removing short artifacts where data loss in that time window is not important, or where artifacts are inconsistent. Dirk Bucher (2012). General Use

artiSubtr - Removes stimulus artifacts from recording traces by subtracting a template average artifact waveform. Useful for removing artifacts with minimal data loss in traces with consistent artifact waveforms. Dirk Bucher (2012). General Use

chunkreplace - Copies a chunk of waveform from one channel and place it into another channel. Dirk Bucher (2012). Fast Hack

ClearProc - Clears all Channel Processes (like "smooth" or "rectify") from all channels. Dirk Bucher (2012). General Use

EditEvt - Allows to delete or add events or markers from event or marker channels "by hand". Dirk Bucher (2007). General Use

setBursts - Generates an event channel with "artificial bursts". Useful for generating test data sets. Dirk Bucher (2002). General Use

subtrSpikes - Subtracts events of one channel from another. Dirk Bucher (2002). General Use

WinSubtr - Deletes events in an event channel in time windows defined by markers in a marker channel. Dirk Bucher (2004). General Use

 

File Manipulation

batchImp - Converts a batch of files in foreign format (e.g., Axon) into spike2 files. Dirk Bucher (2002). General Use

ConcatFiles - Concatenates consecutive time view files (waveform channels only). Dirk Bucher (2007). General Use

RepFileMerge - Creates a new file that holds event and waveform channels from two source files that were recorded with matching stimulus patterns. Channels aligned at reference stimulus patterns can then be used for virtual channel calculations. Dirk Bucher (2013). General Use

 

Plot

EMFseq - Outputs a sequence of metafiles from time views. Useful for making movies or images of longer time stretches at decent resolution. CAN NOW EASILY BE EXTENDED TO ALLOW TIFF OR JPG, JUST HAVEN’T DONE THAT YET. Dirk Bucher (2005). Fast Hack

floatingBar - Creates an XY view floating bar chart with error bars. Values are entered manually.Fast way to create phase plots for CPG patterns. Wolfgang Stein & Dirk Bucher (2009). Fast Hack

mSweepAve - Plots multiple sweeps of AVERAGED waveform data with fixed delay and duration from a trigger (XY plot). Dirk Bucher (2014). General Use

multiSweep - Plots multiple sweeps of waveform data with fixed delay and duration from a trigger (XY plot). Dirk Bucher (2002). General Use

PhSweepAve - Creates both a multiple sweeps window and an average of waveform data in phase, i.e. normalized to the sweep duration. Dirk Bucher (2016). General Use

PoissCreate - Makes a file with an event channel in Poisson distribution. Dirk Bucher (2016). General Use

respMk - Creates artificial unitary passive responses from spike train event channel input using a te-at function. Useful to create artificial EPSP or contraction responses to a spike pattern. Ralph DiCaprio & Dirk Bucher (2002). General Use

SquareWave - Creates a waveform channel with square signals, at time points taken from an event channel. Dirk Bucher (2013). Fast Hack

SweepAve - Plots average from multiple sweeps in XY file. Only uses visible channels. Dirk Bucher (2016). General Use

SweepDiff - Plots the difference between two multisweep plots, as generated with "MultiSweeps". Useful for leak subtraction and difference currents from VC protocols. Dirk Bucher (2004). General Use

TrigEMF - Outputs a sequence of metafiles from time views triggered by events. Useful for making movies or images of longer time stretches at decent resolution. CAN NOW EASILY BE EXTENDED TO ALLOW TIFF OR JPG, JUST HAVEN’T DONE THAT YET. Dirk Bucher (2005). Fast Hack

WolfieSweep - Version of "multisweep" for more than 2 channels. Wolfgang Stein (2005). General Use

XYIhleak -Subtract leak from Ih measurements by scaling the response to the smallest command and subtracting it from all step responses. Alternative to subtracting leak from backward fits (script”Ih_fit”) under waveform analysis. Dirk Bucher (2016). Fast Hack

 

Spike Analysis

burstDelay - Analyzes delays and spike waveforms from burst stimulations of axons. Dirk Bucher (2012). Specialized

delFilter - Sorts spikes according to 2 different delay times between 2 recording sites. Dirk Bucher (2002). General Use

delFix - Plots delays between stimuli and spike responses, lets you edit for spike failures and ectopic spikes. Dirk Bucher (2016). Specialized

delPlot - Plots delays between stimuli and spike responses into a RealMark channel. Dirk Bucher (2012). Fast Hack

delTest - Plots delays between stimuli and spike responses into a RealMark channel, even if number of events are not matching. Useful for identifying spike failure times.Dirk Bucher (2012). Fast Hack

FailEctZoom - Checks for spike failures or ectopic spikes in burst stimulations, and zooms in on the next occurence of a mismatch between stim and response event channels. Dirk Bucher (2011). Specialized

IF_ISI - Returns intervals and instantaneous frequencies for an event channel.Dirk Bucher (2002). Fast Hack

PoissDel - Analyzes delays and spike waveforms from poisson stimulations of axons. Dirk Bucher (2012). Specialized

pPulse - Analyzes spike delays and waveform parameter changes from paired pulse recovery cycle protocols. Dirk Bucher (2010). Specialized

rate_meanfreq - Returns spike numbers and mean frequency in defined bins from an event channel.Dirk Bucher (2002). Fast Hack

tPulse - Analyzes spike delays and waveform parameter changes from recovery cycle protocols with conditioning trains. Dirk Bucher (2010). Specialized

 

View Manipulation

ChanWeight - Sets the relative vertical space taken up by a channel. Dirk Bucher (2007). General Use

CurLabelSwitch - Switches cursor label mode between "no label", "position only", "number only", and "position (number)". Dirk Bucher (2012). General Use

DelCur - Deletes all cursors (vertical and horizontal). Dirk Bucher (2002). General Use

displSwitch - Switches between default font and font sizes and larger fonts. Dirk Bucher (2003). General Use

optimise - Optimizes y-range for all channels. Similar to Ctrl+Q, but optimizes all channels, even unselected ones. Dirk Bucher (2002). General Use

TimeMax - Maximizes x-axis.Dirk Bucher (2002). General Use

 

Waveform Analysis

aab - Measures area above baseline (voltage integral) for single or compound EPSPs or EJPs.Dirk Bucher (2002). General Use

ClearFit - Removes all fits from all channels in result view or waveform channels or XY plots.Dirk Bucher (2009). General Use

decayfit - Returns time constants from dual exponential fits for PSPs or spikes as marked with event channel.Dirk Bucher (2010). Fast Hack

Ih_fit - Measures IV values, time constants and tail currents from multisweeps of non-leak subtracted Ih Vclamp data. Dirk Bucher (2008). Specialized

IMI_XYcursors - Drops cursors into an XY view IV plot of IMI for fast measurements, returns values to log window. Dirk Bucher (2013). Fast Hack

IMIcont - Creates IV plots of the modulator activated inward current from continuous (repeated) voltage clamp ramps during peptide application. Dirk Bucher (2012). Specialized

instCorr - Creates fast scatterplots of EPSP or EJP amplitudes from 2 waveform channels to see if they are correlated. Dirk Bucher (2005). Fast Hack

IVcurve - Returns IV values from time views of step protocols. Dirk Bucher (2004). Fast Hack

P5protocol - Creates a multisweep xy view of the summed step sequence from P/5 protocol data. For leak subtraction using the "SweepDiff" script. Dirk Bucher (2009). Specialized

PPsubtr - Subtracts conditioning pulse waveform from paired pulse responses and does paired pulse analysis.Dirk Bucher (2014). General Use

PSPparamAv - Returns PSP parameters from a waveform average. Dirk Bucher (2002). Fast Hack

RampIV - Creates difference current and IV plot from result files averaged from voltage ramps run to measure IMI in STG neurons. Dirk Bucher (2012). Specialized

SpkShapeSingle - Returns spike shape or EPSP shape parameters like peak voltage, time to peak and 2 time constants of exponential decay. Dirk Bucher (2014). Fast Hack

SynVC - Modification of "XI_IVcurve", specifically for synaptic currents from VC expts. Useful for analysis of slow graded synaptic currents in STG neurons. Ayanna Bryan & Dirk Bucher (2010). Specialized

trainPSPamp - Measures the amplitudes of PSPs in trains or bursts.Dirk Bucher (2002). General Use

TrigPSP - Returns PSP parameters for separate events.Dirk Bucher (2002). General Use

WaveToEv - Does event detection from waveform channel (peak, trough, threshold) and writes results into real event channel. Dirk Bucher (2002). General Use

winDiscr - Window Discriminator for event detection based on horizontal cursors. Dirk Bucher (2002). General Use

XY_IV - IV measurements from VC or CC step protocol data in XY views created with “multiSweeps”. Dirk Bucher (2013). General Use

XY_TabOut - Outputs xy view data as a text file with tab separated columns. Dirk Bucher (2009). Specialized

 

Scope software for data acquisition (Version 8.07; Needs National Instruments Data Acquisition Board and NI-DAQmx). © 2014, STG Lab. Last update: 07/30/14+

Scope is data acquisition software developed by our lab in Lab Windows/CVI (National Instruments, TX). It is used to acquire electrophysiological data. It offers functionality of traditional strip chart recorder and oscilloscope. Scope can acquire up to eight input channels simultaneously. It displays data from acquired channels in real time. Acquired data can also be saved on disk in binary format with a header to store information about the data. The data file is named using yyyy_mm_dd_hh_mm_ss.scp convention. Scope also offers various options such as filters, Fourier transforms, unit conversions etc. Scope works on windows with E series analog to digital conversion boards of National Instruments.   DOWNLOAD  

ReadScope software for data analysis (Version 8.02). © 2014, STG Lab. Last update: 07/30/14+

Read Scope is data analysis software developed by our lab in Lab Windows/CVI (National Instruments, TX). Scope and Dynamic Clamp software save electrophysiological data in binary format on the disk. These data files can be viewed using Read Scope. The data file is named using yyyy_mm_dd_hh_mm_ss.scp convention. The file contains fixed format header with information about the data. Read Scope decodes the header and displays the data. Read Scope offers various options such as filter, Fourier transforms, extracting spikes, calculating area under curves etc. Read Scope works on windows operating system.   DOWNLOAD  

DataMaster software for data analysis (Version 2.2). © 2014, STG Lab. Last update: 07/30/14+

DataMaster is a program to perform phase analysis and simple frequency analysis of one or more periodic (i.e. bursting) signals.   DOWNLOAD  

PhaseResponse software for PRC stimulation (Version 2.01). © 2014, STG Lab. Last update: 07/30/14+

Phase Response is a software that injects waveforms (pulse, sine, etc.) at a fixed phase or time delay into an oscillating neuron. The waveform can be injected as current or conductance (i.e. dynamic clamp). The injection could be once or multiple times (entrainment). If a fixed phase is chosen for the waveform stimulus, the time delay to the beginning of the stimulus is calculated using the previous cycle period. The program can inject the stimulus from the beginning or end of a "burst" for a bursting neuron. If the neuron is only spiking, the detection parameters should be adjusted to allow for individual spikes to be considered a burst.   DOWNLOAD  

HHfit software for ionic current fits (Version 3.2). © 2014, STG Lab. Last update: 07/30/14+

HHfit is a program to manually fit ionic currents to obtain parameters for dynamic clamp.

For automatic fits, we recommend NetFit.

Network software for neural simulations (Version 2.09). © 2014, STG Lab. Last update: 08/13/14+

Network is a no-frills neural simulation software that is user-friendly and produces text files (not fancy plots or diagrams) as output. network only runs in linux or a linux-compatible environment such as the linux-emulator cygwin in MS Windows, in Mac OS X or any Unix OS that includes bash, gawk, gcc and make.

Network source code and executables (current version 2.09):   tgz   or   zip  

Network Manual (not updated since version 1.40):   pdf  

Some examples and tutorials:   tutorials   ,   synapse  

The tgz files need to be expanded in Linux.

The pdf file is the user's manual which is somewhat incomplete but should get you off the ground.

To install network, copy the file network209.tgz into some directory in linux, login as root and type:

cd /usr/local

tar zxvf "directoryname"/network209.tgz

where "directoryname" is the name of the directory where network209.tgz was put in (e.g. /home/nick).

To expand the tutorials copy the file tutorials.tgz into a directory (e.g. your home directory) and type:

tar zxvf tutorials.tgz

This puts each tutorial in a subdirectory.

Alternatively, you can unzip the files and put them in some directory and add the directoryname to your path.

– Dynamic Clamp software is no longer supported. We recommend using NetClamp instead.

– For more information on National Instruments DAQ boards, please visit www.ni.com.

– For help regarding installations and use of the software, please e-mail Farzan Nadim.

 

Protocols & Recipes

Salines – Recipes for several species+.

 

If you don't trust yourself to calculate the correct weights for a given molarity, go here:   Molarity Calculator  

 

Download all as PDF or Word file.

Cancer borealis

Normal saline

Salt (FW) Conc [mM] g/l g/6l g/11l
KCl (74.56) 11.0 0.82 4.92 9.02
NaCl (58.44) 440.0 25.71 154.28 282.85
CaCl2 · 2H2O (147.02) 13.0 1.91 11.47 21.02
MgCl2 · 6H2O (203.31) 26.0 5.29 31.72 58.15
Trizma base (121.14) 11.2 1.36 8.14 14.92
Maleic acid (116.07) 5.1 0.59 3.55 6.51
Hepes (instead of Tris+Maleate) (283.3) 10.0 2.83 17.00 31.16

pH = 7.4 - 7.5; Osmolarity = 1030 mOsm

Mn2+ saline

Salt (FW) Conc [mM] g/l g/2l g/5l
KCl (74.56) 11.0 0.82 1.64 4.10
NaCl (58.44) 440.0 25.72 51.43 128.57
CaCl2 · 2H2O (147.02) 0.1 0.015 0.029 0.073
MgCl2 · 6H2O (203.31) 26.0 5.288 10.575 26.438
Trizma base (121.14) 11.2 1.358 2.715 6.788
Maleic acid (116.07) 5.1 0.593 1.185 2.963
MnCl2 · 4H2O (197.9) 12.9 2.55 5.10 10.20

pH = 7.4 - 7.5; mix and dissolve completely, then pH, and ONLY THEN add the Mn2+!

Supplement solution (to mix 50:50 with L-15 culture medium):

Salt (FW) Conc [mM] g/l g/½l g/¼l
KCl (74.56) 16.40 1.22 0.61 0.305
NaCl (58.44) 743.66 43.46 21.73 10.865
CaCl2 · 2H2O (147.02) 24.74 3.64 1.82 0.909
MgCl2 · 6H2O (203.31) 50.20 10.21 5.10 2.552
Hepes (283.3) 10.0 2.83 1.42 0.708

Zero Ca2+ / zero Mg2+ dissociation solution

Salt (FW) Conc [mM] g/l g/½l g/¼l
KCl (74.56) 11.0 0.82 0.41 0.205
NaCl (58.44) 440.0 25.71 12.86 6.43
Hepes (283.3) 10.0 2.83 1.42 0.708

 

"Elixir" Saline (for long-term recordings of crab or lobster STG)

For 100ml crab or lobster saline:

—   0.2g Glucose (11.11mM)

—   4.5g BSA

—   0.5g antibiotics

 

Panulirus interruptus / Homarus americanus

Normal saline

Salt (FW) Conc [mM] g/l g/6l g/11l
KCl (74.56) 12.8 0.95 5.73 10.50
NaCl (58.44) 479.0 27.99 167.96 307.92
CaCl2 · 2H2O (147.02) 13.7 2.01 12.09 22.16
MgSO4 · 7H2O(246.48) 10.0 2.46 14.79 27.11
NaSO4 · 10H2O(322.20) 3.9 1.26 7.54 13.82
Trizma base (121.14) 11.2 1.36 8.14 14.92
Maleic acid (116.07) 5.1 0.59 3.55 6.51
Hepes (instead of Tris+Maleate) (283.3) 10.0 2.83 17.00 31.16

pH = 7.4 - 7.5; Osmolarity = 1050 mOsm

Mn2+ saline

Salt (FW) Conc [mM] g/l g/2l g/5l
KCl (74.56) 12.8 0.96 1.91 4.78
NaCl (58.44) 479.0 27.99 55.99 139.97
CaCl2 · 2H2O (147.02) 1.3 0.19 0.38 0.95
MgSO4 · 7H2O(246.48) 10.0 2.47 4.93 12.33
NaSO4 · 10H2O(322.20) 3.9 1.26 2.51 6.28
Trizma base (121.14) 11.2 1.36 2.71 6.78
Maleic acid (116.07) 5.1 0.59 1.18 2.96
Hepes (instead of Tris+Maleate) (283.3) 10.0 2.83 5.67 14.17
MnCl2 · 4H2O (197.9) 16.0 3.16 6.32 15.80

pH = 7.4 - 7.5; mix and dissolve completely, then pH, and ONLY THEN add the Mn2+!

 

 

Procambarus clarkii

Normal saline

Salt (FW) Conc [mM] g/l g/2l g/6l
KCl (74.56) 5.4 0.403 0.805 2.416
NaCl (58.44) 195.0 11.396 22.792 68.375
CaCl2 · 2H2O (147.02) 13.5 1.985 3.970 11.909
MgCl2 · 6H2O(246.48) 2.6 0.529 1.057 3.172
Trizma base (121.14) 11.2 1.357 2.713 8.141
Maleic acid (116.07) 5.1 0.592 1.184 3.552
Hepes (instead of Tris+Maleate) (283.3) 10.0 2.833 5.666 16.998

pH = 7.4 - 7.5

Supplement solution (to mix 50-50 with Leibovitz L15 culture medium):

Salt (FW) Conc [mM] g/l g/½l g/¼l
KCl (74.56) 4.64 0.346 0.173 0.086
NaCl (58.44) 253.10 14.791 7.396 3.698
CaCl2 · 2H2O (147.02) 24.74 3.637 1.819 0.909
MgCl2 · 6H2O(246.48) 4.22 0.858 0.429 0.214
Hepes (283.3) 10.0 2.833 1.417 0.709

 

 

Other Solutions – Buffer, fixatives, etc.+

 

If you don't trust yourself to calculate the correct weights for a given molarity, go here:   Molarity Calculator  

 

Download all as PDF or Word file.

0.1M Phosphate buffer solution

—   Prepare 4 volumes (800 ml for 1l) of 0.1 M sodium phosphate dibasic (Na2HPO4).

—   Prepare 1 volume (200 ml for 1l) of 0.1 M sodium phosphate monobasic (NaH2PO4).

—   Mix 4 parts of the dibasic solution with 1 part of monobasic to make a final 0.1M phosphate solution.

—   Adjust the pH to 7.3-7.4

0.1M Phosphate buffer solution + 0.3% Triton-X

—   Use the phosphate buffer made as indicated above and add Triton-X to a final concentration of 0.3% (i.e. 0.3 ml in 100 ml solution).

 

Bouins fix

Preparation (for 1 liter):

—   Measure 750ml filtered saturated picric acid

—   Add the picric acid to 250 ml of 40% formalin

—   Add to the mixture above 50ml glacial acetic acid

—   Stir until mixed

Store at room temp; stays good forever.

Note:

—   ALWAYS put the date on a freshly made solution. Also add your initials, pH and concentration.

—   Label anything that touches fixative solution with the words FIX (or something like that). Dishes or stirrers once used for fix should not be used to make non-fix solutions such as salines!!!

 

4% Paraformaldehyde solution

Preparation (for 1 liter):

—   Prepare 4 volumes (800 ml for 1l) of 0.1 M sodium phosphate dibasic (Na2HPO4).

—   Prepare 1 volume (200 ml for 1l) of 0.1 M sodium phosphate monobasic (NaH2PO4).

—   Warm the dibasic phosphate solution to 60°C.

—   Weigh the paraformaldehyde (i.e. 40g for a 1l solution, 4g for a 100ml solution).

—   Add to the warm dibasic phosphate stirring constantly (do not exceed 70°C; if you do, then start again).

—   When paraformaldehyde has disolved (should take ~ 5min) add the monobasic phosphate solution.

—   The pH should be about right, but check it. If not correct, then add NaOH or HCl to bring it to 7.4.

—   If the solution has been heated for too long, white flakes may appear. If there are a lot, start again. If there are only a few, filter the solution.

—   Add 400mM sucrose (this is to adjust the osmolarity of the solution to something close to the saline's).

Troubleshooting

—   Paraformaldehyde (the powder) reacts readily with oxygen and oxidizes to a less active form. Thus, in order to preserve it in the best possible condition it should be weighed in aliquots (2 or 4 grams, for example), packed tightly to eliminate as much air as possible (ideally in a N2 atmosphere), sealed in small container and stored frozen.

—   Paraformaldehyde solutions go bad rapidly. Thus, ALWAYS put the date on a freshly made solution, and throw the solution away after 1-2 days.

—   Label anything that touches fixative solution with the words FIX (or something like that). Dishes or stirrers once used for fix should not be used to make non-fix solutions!!!

Alternatively, use premade Paraformaldehyde from Electron Microscopy Science and dilute it with phosphate buffer.

 

15% Picric acid + 2% Paraformaldehyde fix

Preparation:

—   Carefully heat up 15ml double filtered saturated picric acid to 60°C.

—   Add 2g paraformaldehyde (it will get all thick and cloudy).

—   Slowly add strong NaOH (5N) until everything is in solution. "Clear" is when you can't see any more particles in the picric acid. The original recipe calls for 2.52% NaOH but it does not have to be exacly 2.52%.

—   Filter again and fill to 100ml with phosphate buffer and keep at 4°C in a dark bottle.

—   Make sure pH is ~7.3.

Note:

—   ALWAYS put the date on a freshly made solution. Also add your initials, pH and concentration.

—   Label anything that touches fixative solution with the words FIX (or something like that). Dishes or stirrers once used for fix should not be used to make non-fix solutions!!!

 

Ice-cold ethanol fix

Preparation (for 1l):

—   Prepare 95% Ethanol solution. Ethanol can be bought at a concentration of 100% percent, which is called anhydrous or denatured. In this case it has to be diluted to 95%. It can also be obtained at 95%. 95% is the highest concentration that ethanol can be destilled to. To make it completely free of water a chemical process is used that may add traces of chemicals to it. So the best is to simply get destilled ethanol. It is also much cheaper.

—   Cool it to about 0°C (placing it in ice water is the most effective way).

—   Rinse your preparation a few times with this ethanol solution and then leave it on ice for 1-2 hours. Depending on the thickness of the tissue. For STGs it seems to work OK if fixed for 1 hour. If you leave it on ice, make sure that the ice is wet so that the temperature will indeed be kept at ~0°C, but make sure that your dish does not sink into the ice (which may happen if you are using the dissection Petri dish for this).

—   Rinse 2-3 times every 60 minutes in phosphate buffer + Triton X (if you are proceeding with immunostaining) or plain phosphate buffer if you are doing something else

Keep your Ethanol solution sealed to prevent Ethanol evaporation. Since Ethanol and water evaporate at different rates, the EtOH concentration can change quite a bit. The tissue becomes white and hard in EtOH but becomes translucent and soft again when washed in phosphate buffer. It tends to stick to the walls of the plastic containers, etc. much more than when using aldehyde fixes.

Note:

—   ALWAYS put the date on a freshly made solution. Also add your initials and concentration.

—   With this particular fix, you can use your standard physiology dishes and tools. EtOH evaporates and and very low concentrations is completely harmless.

 

Stainless Steel solder

Solution good for soldering stainless steel, tungsten, nichrome, possibly even niobium. It really cuts through oxides. CAUSTIC, CORROSIVE. Wear safety glasses, etc.!!!

Used to make non-corroding electrodes (stainless steel) corrosibles.

Important:Use ORGANIC CORE SOLDER. Do NOT use the standard rosin core solder (the one that has a resin core and used for tin soldering). This one contains an organic (water soluble) core.

Jesse's Super Flux (Don't ask who Jesse is!):

96g ZnCl2

9.6g NH4Cl

25ml H2O

10ml HCl (conc.)

 

Protocols – Staining, mounting, etc+.

Generic STG immunohistochemistry protocol.   PDF     Word  

Intracellular dye filling.   PDF     Word  

Clearing tissue and mounting preps.   PDF     Word  

TechSpecs – Rig gadgets, etc+.

A collection of instructions for building stands, holders, etc., mainly intended as specifications for the machine shop.

2 different designs for dish holders / rig stages.   PDF  

3 different designs for Peltier holders.   PDF  

2 different designs for mirror and darkfield condenser holders.   PDF  

Plexiglass dissection stand.   PDF  

Aluminum sheet Faraday cage.   PDF  

RC filter for Axoclamp V2 output.   PDF  

The Axon Guide.   PDF  

The Sutter P-97 Pipette Cookbook.   PDF (2008)     PDF (2015)  

Spike2 / CED 1401 sampling configurations for Axoclamp 2B amplifiers   PDF  

Floating electrodes.

(Reference: Vivian Budnik)

 

–   Pull an electrode in the customary way.

–   Backfill it with the chosen electrolyte.

–   Brake the tip with a fine file at approximately the level were the taper begins (hold the tip with soft forceps).

–   Insert the tip into the Ag wire and seal the end against the wire with plasticine (or wax, etc).

–   The Ag wire should be very thin and Teflon coated to add strength and flexibility.

–   The very tip should then be stripped of the Teflon and chlorided with bleach (10-15min in bleach) or electrolytically.

–   The wire should be supported by a rod attached to the headstage of the amplifier and connected to the headstage; the freely hanging part should only be a few millimeters long (perhaps up to 1 cm) impale as usual: approach and buzz.

 

 

STG References, Figures & People

STG References –The (incomplete) library of STG publications+.

The link below points to a separate page that lists a large number of STG publications, the majority with PDF files. It also provides a downloadable zip file containing an EndNote library with attached PDFs.

For legal reasons, the page is passworded. Hint: What is the abbreviation for the pacemaker interneuron of the pyloric circuit?

  Go To Page  

STG Guides – Anatomy and Example Recording Traces+.

Cancer borealis STG Guide   PDF  

Homarus americanus STG Guide   PDF  

Callinectes sapidus Guide   PDF  

STG Figures – A Collection of JPG, Canvas, and CorelDraw files.+

Click on icon to open full JPG image in new window. To download, right-click on icon and select "save link as...".

This collection is intended to be a repository for general STG figures, to be freely used by anyone. That said, there are some figures in here (and more may follow) that are from publications or have been made in the past by people we did not specifically ask for permission. Please use your own best judgement in acknowledging the source when you use them. If you have any concerns, please email Dirk Bucher.

Anatomy, Cancer borealis. By Veronica Garcia.

Anatomy, Homarus americanus. Modified from Marder & Bucher (2007), after Herrick (1909).   Canvas  

Stomach with nerves and muscles, Homarus americanus. Modified from Bucher et al. (2006), after Maynard & Dando (1974).   Canvas  

Stomach muscles and nerves, Cancer borealis. Modified from Weimann et al. (1991).

STNS (1), Cancer borealis.

STNS (2), Cancer borealis.

STNS (1), Homarus americanus. Bucher et al. (2006).   Canvas  

STNS (2), Homarus americanus. By Dirk Bucher.   Canvas  

Circuit diagram, Cancer borealis. Modified from Marder & Bucher (2007), after Nusbaum & Beenhakker (2002).   Canvas  

Core pyloric circuit.By Dirk Bucher.   Canvas  

Neuromodulators, Cancer borealis. Modified from Marder & Bucher (2007).   Canvas  

Darkfield image of the STG, Cancer borealis.

Gastric mill teeth, Panulirus interruptus. From Marder & Bucher (2007).

Somata map, Homarus americanus. From Bucher et al. (2007).

Other Labs – STG labs, friends & collaborators+.

 Deborah Baro  Georgia State University

 John Birmingham  Santa Clara University

 Dawn M. Blitz  Miami University

 Amitabha Bose  New Jersey Institute of Technology

 Ralph A. DiCaprio  Ohio University

 Patsy Dickinson  Bowdoin

 Ronald Harris-Warrick  Cornell University

 Daniel K. Hartline  University of Hawaii

 Scott L. Hooper  Ohio University

 Lingjun Li  University of Wisconsin-Madison

 Victor V. Matveev  New Jersey Institute of Technology

 Eve Marder  Brandeis University

 Brian Mulloney  UC Davis

 Michael P. Nusbaum  University of Pennsylvania

 Astrid Prinz  Emory University

 Horacio G. Rotstein  New Jersey Institute of Technology

 David J. Schulz  University of Missouri

 Tomasz G. Smolinski  Delaware State University

 Wolfgang Stein  Illinois State University

 Carmen Wellmann (Smarandache)  University of Cologne