Software for Brain Slice Physiology



About Slice™

Slice™ is a complete IGOR software package created by Fanyee Anja Lee, Chris DiMattina, and Dan Sanes for the purpose of providing a data acquisition and analysis system for in vitro slice physiology.

In particular, this system gives users the ability to stimulate two afferent fiber pathways and to record intracellular synaptic events in single neurons using either current- or voltage-clamp configurations.

Figure 1: A schematic of the experimental setup

In addition to stimulus isolation units and Patch Clamp Amplifier (we use a Warner 501A), Slice™ requires the following hardware and software:

* IGOR version 4.0.5 or later from WaveMetrics,Inc.(http://www.wavemetrics.com/)

* A Power Macintosh running OS 10.2.x or later.

* An ITC-18 data acquisition interface and a PCI-18 host bus adapter card from Instrutech,Inc. (http://www.instrutech.com/)

* IGOR ITC-18 XOP from Instrutech. This can be downloaded below along with the Slice™ program. It is placed in the Igor Extensions folder.

* An adder is required for some experimental setups

Slice™ supports many different experimental paradigms (see User's Manual) in a turn-key freeware package. Furthermore, it may be modified and upgraded by the sophisticated IGOR user to suit his or her needs.


Figure 2: The Slice stimulus setup window

Figure 3: The Slice stimulus preview window

 

Figure 4: The Slice data acquisition window

 

Slice Analysis Program

 

In order to analyze data that is collected and stored with Slice, we have written a program that performs the following basic analyses:

1) IV curves and time constants

2) Reversal potentials

3) Spike times

4) Analyses of synaptic events for five different experimental protocols. Includes: latency to rise, latency to peak, latency to fall, peak amplitude, area, rising slope, duration, rise time, and decay time.

 

Download Slice Files

Slice Software and Manuals [ Download Disk Image ]

READMEs

1) Read ME First

2) READ ME SLICE

Manuals

1) Slice 1.2 User Manual [ PDF ] [ WORD ]

2) Slice Tech Manual [ PDF ] [ WORD ]

3) Slice II Analysis [ PDF ] [ WORD ]

 

Legal Notices and Technical Support

Grant Citations

NOTE: This software is free, and may be modified by the user. Any publication that results from use of this software (or >50% of the code) should cite the NIDCD grant that paid for its development: DC00540

Technical Support Disclaimer

We do not offer any technical support for this program. It has been documented and tested in our laboratory for several months, but as with all software, you run at your own risk.

However, since one of us here is a nice person (Fanyee Anja Lee) she is willing to answer technical questions via e-mail, and to correct any bugs or errors in the program. Please e-mail your technical questions to Fanyee Anja Lee (anjaleef@cns.nyu.edu). General questions can be addressed to Dan Sanes (sanes@cns.nyu.edu).