Added plotting script for desynchronisation simulations. Also, enabled GJ connection strengths to be all different from each other.
Manipulating heterogeneity of GJ connectivity as a graph-theoretical degree distribution.
Added plotting script for single cell current-voltage relationship.
Coupling strength simulation and plotting scripts.
Added current-voltage relation plotting script.
The current-voltage relation (and, consequently, the input resistance) doesn't seem to exhibit any significant heterogeneity induced by the gap junction distribution.
Added simulation script for input resistance heterogeneity analysis.
Analysis and plotting script is still to be implemented.
Added network (de)synchronisation analysis as in Vervaeke2010.
Two new simulation configurations, network_desynchronisation and network_desynchronisation_2010gap, try to reproduce the desynchronisation effect reported in Vervaeke2010. The expected behaviour seems to emerge only if the gap junction connectivity is...
Fixed missing GJ netconn and generally improved GJs for reduced model.
Now the first segment of the apical dendrites in the reduced model is considered as being still in the molecular layer. This is to better reproduce the choices made for the detailed model, and it plays an...
Rate-coded I/O analysis for parallel fibre input, with gap junctions.
Rate-coded I/O analysis for mossy input, with gap junctions.
The gap junctions, the network and the stimuli are implemented as in Vervaeke2012, except for heterogeneity. The detailed cell model replicates the results in the paper, and the simplified one seems to...
Renamed FI curve script. Added FI results plot to the repo.
Another attenuation estimate (same cells, new random probe placement).
The agreement between the models is good, and they are both quite close to the 52 micron experimental estimate in Vervaeke2012, figure 3C.
Updated attenuation result with latest version of the model.
Deleted old version of attenuation scripts and renamed the 'good' one.
The version that got deleted was confusing, as it wasn't immediately clear that it didn't have anything to do with the results in Vervaeke2012. Also, accordingly renamed the figure showing the...
Updated attenuation analysis to work with the latest model version.
Also, added some comments to make clearer which script is the one to be used to benchmark the model's behaviour against Koen's paper.
Reduced the basolateral dendrites' size.
This results in a better match for rate-coded I/O relationship for mossy fiber stimulation, but on the other hand the cell is now responding too much to apical stimulation. Also, the spike shape is less bad (the size of the little after-spike hump has decreased).
Enabled effective remote simulation for fi curve script.
Added: rate-coded I/O comparison (Vervaeke, Solinas and reduced).
Added various relevant scripts and nC project elements. Note that the existing nework connections in the nC project have been renamed, and this might have broken some of the old scripts.
At this point, the results of the rate-coded I/O relationship are:...
Updated segment groups.
Raised the simulation temperature to 30 degrees.
Rotated reduced model so that it points in the correct direction.
Minor simulation/plotting improvements.
Added plotting of detailed model's potential in spontaneous firing simulation, and aligned the stimulation points for the detailed cell in attenuation.py so that they match those that I'm forced to use in the simplified cell.
Fixed 'double spike' bug caused by on old KBK channel implementation.
This is a well-known problem with an old version of the mod file for the KBK channel, and had been squashed somewhere else (at least in the original model by Solinas - see relevant files on ModelDB and Open...
Formatting: preparing to modify KBK channel.
Modified axon and bl dendrites. Looking better.
Things that have improved: - resting potential (closer to Koen's model) - somatic response to single synaptic input on a dendrite (closer to Koen's model, but still a bit too weak) - spike shape (actually starting to look as "halfway between" Koen's...
Making larger changes in morphology beyond the apical dendrites.
I managed to get the dendritic attenuation length to match between the models, but the absolute response properties of the cell to synaptic input are still quite different (Koen's model is more reactive to...
Made the second apical dendrite identical to the first one.
Added two new scripts to better reproduce figure 3C in Vervaeke2012.
Koen clarified via email that the cell being tested was 210710_C1, that the attenuation was measured over an apical dendrite (one that he could have pathced during the experiments), and that it wasn't...
Minor: removed superfluous line.
Minor fitting and plotting adjustments.
Created a segment group for each of the apical dendrites in C1.
Added a (0,1) point in attenuation fit because of normalisation.
Added a new segment group representing a single apical dendrite.
Revert "Begun importing other version of detailed morphology GoC."
This reverts commit be055a8cbbf8955c1fc67608f7be31bddc890804.
Begun importing other version of detailed morphology GoC.
Varying the number of stimulation points on the detailed dendrites.
Still fairly hard-coded, but at least I now have more than 3 points for the exponential fit on the detailed morphology.
Removed recording of superfluous data during simulations.
Scripts seem to be working fine.
Attenuation seems to match between the two models (at least with the 4-5-6 dendrite on the reduced morphology and a specific choice of compartments on the detailed one), but they both seem to give different results than those in the paper.
Tidied up the code.
Working on the simulation/analysis scripts.
Added plotting of dependance of maximum somatic response amplitude on distance of stimulation along the dendritic tree.
Leak conductance on both models has been set to 6.67e-10mSum-2, as per supplementary information (page 3) in Vervaeke2012, where 15kOhmcm2 was reported from unpublished observations.
Also, fixed the (wrong) number of internal divisions of a segment.
Still playing around with reduced morphology. Added an axon.
Playing around with morphology to see effects on FI and attenuation.
Adjusted spike detection threshold to avoid picking up doublets in the Vervaeke cell when calculating the F-I curve.
Added scripts for simulating and plotting an F-I curve comparison.
Integrating fast segment-to-soma distance calculation in nC allows to meaningfully compare dendritic attenuation effects on different (and complex) morphologies.
Fixed a remaining issue with the detailed morphology cell.
Note that I turned off again all Na channels.
Now pure NeuroML morphology read/write seems to be working fine, except that it removes property elements tagged 'comment'. This will need to be fixed in neuroConstruct, but doesn't have...
Reverted morphologically-detailed cell model back to its original form to fix some issues (namely, loss of 'number of internal divisions' properties) generated when doing NeuroML write/read with older versions of neuroConstruct.
Modified leak conductance to match what Koen did.
Comparing attenuation in the original (Koen's) model and in my reduced one.
Important: to get to a meaningful comparison, I'm tweaking the spatial discretisation of the original model.
Simulating attenuation for original Golgi model (Na channels switched off as per TTX)
Added a new simulation configuration where GJGolgi_Reduced is simply left alone.
Actual reference morphologies.
Committing reference morphologies, now that neuroConstruct has been fixed to not shuffle channels and synaptic types in NeuroML serialisations and to keep track of the number of internal divisions in each segment. See r1686 and r1689 in nC's svn repo.
Now the location of the synaptic input can be changed, and can be iterated over. Also added a simple plotting script.
Trying to script an attenuation-length analysis that could be compared to Koen's 2012 paper.
The script itself is not yet usable. I have imported a cell from Vervaeke2012 (mainly for the synaptic model, but also to keep it there as a comparison) and a spike relay that I need to simulate a single...
Initial commit: nC project.
Initial commit: ignore file.