Search found 42 matches

by bsuter
Mon Feb 04, 2013 2:54 am
Forum: Parallel NEURON
Topic: Multisplit single cell with many synapses
Replies: 4
Views: 3551

Multisplit single cell with many synapses

Hello, 1. I've made a multi-compartmental single-cell model neuron that runs without error with multisplit over 6 processors (on a single Microsoft Windows/Intel computer). 2. I've added many (e.g. 2000) Exp2Syn point processes to this single cell, distributed across most of the segments, with each ...
by bsuter
Fri Jan 18, 2013 1:42 pm
Forum: Optimization
Topic: Optimizing multiple functions without duplicate runs
Replies: 9
Views: 10604

Re: Optimizing multiple functions without duplicate runs

That's why I suggested the CVode class's record() method. http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/cvode.html#record cvode.record(&rangevar, yvec, tvec, 1) captures rangevar not at the "integration" times, but at the times specified by tvec. It does this by interpola...
by bsuter
Thu Jan 17, 2013 5:03 pm
Forum: Optimization
Topic: Optimizing multiple functions without duplicate runs
Replies: 9
Views: 10604

Re: Optimizing multiple functions without duplicate runs

when the experimental sampling rate doesn't match the simulation time steps (or adaptive time is used): how does one best calculate the error between these time-series (or in the freq domain)? Resample the original data at appropriate intervals. The Vector class's interpolate uses linear interpolat...
by bsuter
Thu Jan 17, 2013 1:19 am
Forum: Optimization
Topic: Optimizing multiple functions without duplicate runs
Replies: 9
Views: 10604

Re: Optimizing multiple functions without duplicate runs

Gotcha, thanks. calculate error measures and add them up I get this conceptually, it's the implementation that poses questions for me. For example, when the experimental sampling rate doesn't match the simulation time steps (or adaptive time is used): how does one best calculate the error between th...
by bsuter
Mon Jan 14, 2013 12:14 pm
Forum: Optimization
Topic: Optimizing multiple functions without duplicate runs
Replies: 9
Views: 10604

Re: Optimizing multiple functions without duplicate runs

Thank you Ted for your quick response. It confirms to me that I can (almost) do what I want, and that's good news :), but also that I'd need to implement my own "error calculation" (objective) functions for each of the measures of interest, and then combine these. As a result, your post has helped m...
by bsuter
Mon Jan 14, 2013 4:53 am
Forum: Optimization
Topic: Optimizing multiple functions without duplicate runs
Replies: 9
Views: 10604

Optimizing multiple functions without duplicate runs

Hello, I've been using the MRF with multiple "Run Fitness" generators. However, now I would like to simultaneously optimize multiple quantities derived from a single simulation run. I'd like to avoid running the simulation more than once for a given set of parameter values. For context: I'd like to ...
by bsuter
Wed Aug 24, 2011 4:53 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28876

Re: Neurolucida to NEURON best practices?

Reconstructions saved in the ASC format from the most recent version of Neurolucida (v10) seem to identify the soma contours with the header "Cell Body", whereas the previous version (v9) used the "CellBody" header. There may be other changes as well - I've requested clarification from MicroBrightFi...
by bsuter
Wed Nov 03, 2010 1:13 am
Forum: MSWin
Topic: Development Enviroments for Windows
Replies: 4
Views: 10151

Re: Development Enviroments for Windows

I've recently started using TextPad on Windows as an editor for hoc, ses, and mode files; there is a free trial version. This editor has tabs for multiple open documents, and also allows side-by-side or top-and-bottom panes for viewing two files simultaneously. There is a built-in file comparison fu...
by bsuter
Tue Nov 02, 2010 1:20 am
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28876

Re: Neurolucida to NEURON best practices?

I believe we've identified sources of some, maybe all, the problems I've encountered. I've succeeded in generating a .hoc file containing the morphology reconstructed in Neurolucida, with minor differences. Some errors remain during the conversion process, but I believe they can be ignored. I believ...
by bsuter
Mon Nov 01, 2010 1:57 am
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28876

Re: Neurolucida to NEURON best practices?

Well, you already fixed one problem by doing the following: Update: Within Neurolucida, I modified the reconstruction such that the soma contours were marked as "Cell Body". While this does not change the geometry of the soma in the reconstruction, it seems to have provided enough identification to...
by bsuter
Sat Oct 30, 2010 1:05 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28876

Re: Neurolucida to NEURON best practices?

My soma reconstruction in NL consists of 19 contours, each in a single z-plane. The generated .hoc for the 3D geometry specification creates 19 sections (soma[0] to soma[18]). Looking at the pt3dadd() calls for these sections, I see the that all points in a single section are at a single z-value, w...
by bsuter
Fri Oct 29, 2010 9:37 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28876

Re: Neurolucida to NEURON best practices?

(Ted, while I was composing this message, you replied to the thread) Update: Within Neurolucida, I modified the reconstruction such that the soma contours were marked as "Cell Body". While this does not change the geometry of the soma in the reconstruction, it seems to have provided enough identific...
by bsuter
Fri Oct 29, 2010 4:01 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28876

Re: Neurolucida to NEURON best practices?

Hi Ted, I'm still trying to get this (Neurolucida to NEURON) to work, but not much luck yet. I'll go back and try to debug from a very simple NL model. I've been using Import3D with a v3 NL .asc file. Most of the "problem points" seem to be at the soma, and in particular where each z-level contour c...
by bsuter
Fri Oct 29, 2010 2:36 am
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28876

Neurolucida to NEURON best practices?

I've completed a detailed reconstruction of a neuron using Neurolucida software. What are current best practices / instructions / gotchas for bringing this morphology into NEURON for simulations? The soma was reconstructed using NL's "contour" mode, i.e. as a sequence of closed polygons, each at a s...
by bsuter
Tue Sep 28, 2010 2:59 pm
Forum: Anatomically detailed models
Topic: File browser dialog missing in Import3D
Replies: 14
Views: 5377

Re: File browser dialog missing in Import3D

Thank you, in this new version the dialogs open on my main screen - works great.