Hi,

Maybe a good thing to do is to fill a neuron by putting biocytin or Alexa antibody in your internal solution when you patch and confirm the locaton afterwards by making slices and histological processing to reveal the neuron´s location. Then you check the slice that contains the neuron in an atlas -Paxinos, for example- and confirm the area of recording.

Another thing you can do in your first trials is to locate the area by means of an injection of a dye in the center of your recording area, for example DiI or pontamine sky blue. DiI is a fluorescent dye in the orange-red range and I guess pontamine sky blue can be seen directly in your slices after cutting, as it acts as an ink -this last statement would require confirmation by an expert-.

I guess you could even deep  with your fingers the tip of a pulled capillary  -I mean if you don´t have a stereotaxic tower-, in the area of recording and filled with the dye.

Good luck!!

Would measuring the latency of the EMG response to the stimulation help? I am not at all an expert, but there may be some useful technical hints here:

http://www.ncbi.nlm.nih.gov/books/NBK3892/

(Methods for Neural Ensemble Recordings, Ch 5, Dzirasa K.)

You mention whiskers - does this mean you want to record in vibrissal (whisker) M1? Or are you interested in forelimb or hindlimb M1? These regions of M1 are in different locations.

For some body parts, microstimulation may be helpful: but it can be difficult to obtain an appropriate level of anesthesia. In addition, electrical microstimulation tends to activate neurons across a large volume (because it activates axons passing through). See for example (Histed, Bonin, Reid, 2010; "Direct activation of sparse, distributed populations of cortical neurons by electrical microstimulation").

I recommend that you use stereotaxic coordinates from existing publications: for whisker M1 in the mouse, perhaps from Karel Svoboda or Carl Petersen. This should be better than relying on an atlas. Paxinos, for example, labels a medial area of cortex "M2", but this is in fact the location where most people place "vM1". Rough coordinates are something like 1.0 mm anterior, 0.9 mm lateral from bregma.

Perhaps have a look at this Shepherd/Svoboda paper - they discuss the anatomical location of vM1, but they also used tracing to/from vM1 and brainstem, as well as functional photostimulation (see Fig. S14).

"Laminar Analysis of Excitatory Local Circuits in Vibrissal Motor and Sensory Cortical Areas" (Hooks et al, 2011, Plos Biol)

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000572

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000572

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874753/

Hi Ping Kwan,

as Marcel suggested, it is a good idea to stain the neuron that you patch for post hoc analysis. We had excellent results by adding 3 mg/ml biocytin to our internal solution. Find more details in: Pernía-Andrade and Jonas. Neuron. 2014 Jan 8;81(1):140-52

Good luck!