edeno/Jadhav-2016-Data-Analysis issues and pull requests

#100 - Ripple Triggered Coherence Plots

Issue - State: closed - Opened by edeno over 7 years ago - 2 comments

#99 - Does canonical group delay exist?

Issue - State: closed - Opened by edeno over 7 years ago

#98 - Create notebook showing group delay with coherence thresholding on simulated data

Issue - State: closed - Opened by edeno over 7 years ago

#97 - Implement clusterless decoding for use on the computing cluster

Issue - State: closed - Opened by edeno over 7 years ago

#96 - Plot ripple-locked coherence averaged over epochs

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment

#95 - Plot baseline coherence

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment

#94 - Add number of pairs per group in coherence plots

Issue - State: closed - Opened by edeno over 7 years ago

#93 - Add code for getting the group delay from significant coherence

Issue - State: closed - Opened by edeno over 7 years ago

#92 - Add code for finding significant coherence

Issue - State: closed - Opened by edeno over 7 years ago

#91 - Plot scatter plot of baseline coherence vs. ripple locked

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment

#90 - Plot time domain signals around ripple

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment

#89 - Plot power spectra of areas

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment

#88 - Double check ground process intensity

Issue - State: closed - Opened by edeno over 7 years ago

#87 - Multi-taper smoothing affects group delay

Issue - State: closed - Opened by edeno over 7 years ago

#86 - Cluster not running the correct version of the code

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment

#85 - Parallelize ripple decoding

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment
Labels: enhancement

#84 - Report coherence or magnitude squared coherence?

Issue - State: closed - Opened by edeno over 7 years ago - 1 comment
Labels: question

#83 - Compute canonical coherence group delay

Issue - State: closed - Opened by edeno over 7 years ago

#82 - scipy.stats.norm.pdf is slow

Issue - State: closed - Opened by edeno over 7 years ago
Labels: enhancement

#81 - Double check the equation for the joint mark intensity

Issue - State: closed - Opened by edeno over 7 years ago

#80 - Double check the concatenation of the ripple spikes

Issue - State: closed - Opened by edeno over 7 years ago

#79 - Parametric bootstrap of Fourier coefficients to capture uncertainty in group delay

Issue - State: closed - Opened by edeno almost 8 years ago

#78 - Eliminate dependencies on data processing module

Issue - State: closed - Opened by edeno almost 8 years ago

#77 - Use EM to estimate replay speed

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#76 - Double check that droping NaNs on ripple locked LFPs makes sense and we aren't losing too much data

Issue - State: closed - Opened by edeno almost 8 years ago

#75 - Deal with symmetry of tetrode pair brain areas

Issue - State: closed - Opened by edeno almost 8 years ago

#74 - Data structure for area pairs in canonical coherence

Issue - State: closed - Opened by edeno almost 8 years ago

#73 - Level names not always in same order

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#72 - Compute group delay on entire session with sliding windows

Issue - State: closed - Opened by edeno almost 8 years ago

#71 - What to use as pre-ripple baseline?

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment
Labels: question

#70 - Fill out Gant chart for Loren

Issue - State: closed - Opened by edeno almost 8 years ago

#69 - Email Shantanu to get the matclust files for the marked point processes

Issue - State: closed - Opened by edeno almost 8 years ago

#68 - File HPc_06_04 isn't running on the cluster

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#67 - Implement canonical coherence on the cluster

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#66 - Handle perfect predictors in GLM fitting

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#65 - Implement spectral granger on the cluster

Issue - State: closed - Opened by edeno almost 8 years ago

#64 - Implement ripple triggered coherence on the cluster code

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#63 - Implement non-parametric spectral granger

Issue - State: closed - Opened by edeno almost 8 years ago

#62 - More stable way to compute the matrix inverse in spectral granger?

Issue - State: closed - Opened by edeno almost 8 years ago

#61 - Use non-parametric version of spectral granger?

Issue - State: closed - Opened by edeno almost 8 years ago

#60 - Proper way to deal with multiple trials in spectral granger?

Issue - State: closed - Opened by edeno almost 8 years ago

#59 - Canonical Coherence is sensitive to the number of electrodes in each group

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment
Labels: question

#58 - Make sure data is centered in the right axis for canonical coherence

Issue - State: closed - Opened by edeno almost 8 years ago

#57 - Memoize spectral functions?

Issue - State: closed - Opened by edeno almost 8 years ago
Labels: enhancement

#56 - Use numpy instead of python lists for input to coherence functions?

Issue - State: closed - Opened by edeno almost 8 years ago

#55 - Replace print statements with logging module

Issue - State: closed - Opened by edeno almost 8 years ago
Labels: enhancement

#54 - Degrees of freedom for GLM spline

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#53 - Linear distance < 0

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment
Labels: bug

#52 - Exclude reference tetrodes in analysis

Issue - State: closed - Opened by edeno almost 8 years ago

#51 - Find out why tetrodes marked "riptet" are better for ripple detection

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#50 - Criterion for neuron exclusion

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#49 - Add session time categorical to the ripple_info data structure

Issue - State: closed - Opened by edeno almost 8 years ago

#48 - Compute spectrogram of ripples in ripple band for CA1 tetrodes

Issue - State: closed - Opened by edeno almost 8 years ago

#47 - Compute coherence by ripple type

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#46 - Take spectrogram of PFC tetrodes on entire experiment

Issue - State: closed - Opened by edeno almost 8 years ago

#45 - Compute canonical coherence

Issue - State: closed - Opened by edeno almost 8 years ago

#44 - Compute spectral granger causality

Issue - State: closed - Opened by edeno almost 8 years ago

#43 - Which frequencies should we focus on?

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#42 - Rename data_filter module to data_processing

Issue - State: closed - Opened by edeno almost 8 years ago

#41 - Make an interactive visualization of the ripple decoding

Issue - State: closed - Opened by edeno almost 8 years ago

#40 - Are there files in the current dataset we can use for marks

Issue - State: closed - Opened by edeno almost 8 years ago - 2 comments

#39 - Are the candripples files the consensus ripples from Loren Frank's lab?

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#38 - Is the encoding model fitting properly?

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#37 - Add to ripple summary statistics: number of spikes per ripple, number of unique spikes per ripple

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#36 - Add 1% of firing rate as an offset as a baseline for the conditional intensity

Issue - State: closed - Opened by edeno almost 8 years ago

#35 - Use clusterless decoding or sorted spikes?

Issue - State: closed - Opened by edeno almost 8 years ago

#34 - Better model for reverse time trajectory for the ripple decoding

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#33 - Figure out how they do their referencing

Issue - State: closed - Opened by edeno almost 8 years ago - 1 comment

#32 - Should we use the Frank lab ripples or the Multitaper ripples

Issue - State: closed - Opened by edeno about 8 years ago - 2 comments

#31 - Use ripple detection method of Kay 2016?

Issue - State: closed - Opened by edeno about 8 years ago - 3 comments

#30 - Apply spectral analysis to different animal / epoch

Issue - State: closed - Opened by edeno about 8 years ago

#29 - Subtract mean when computing the spectrum when computing power differences / coherence differences

Issue - State: closed - Opened by edeno about 8 years ago

#28 - Setup meeting with Loren Frank

Issue - State: closed - Opened by edeno about 8 years ago

#27 - Better function documentation

Issue - State: open - Opened by edeno about 8 years ago - 1 comment

#26 - Rename segments to peri-event window

Issue - State: closed - Opened by edeno about 8 years ago

#25 - Write group delay test code

Issue - State: closed - Opened by edeno about 8 years ago

#24 - Email to figure out how novel is each track exposure

Issue - State: closed - Opened by edeno about 8 years ago

#23 - Normalize the ripples before computing the ripple triggered average LFP

Issue - State: closed - Opened by edeno about 8 years ago - 1 comment

#22 - Compute point process spectra of the start times of the ripple events

Issue - State: open - Opened by edeno about 8 years ago

#21 - Prepare slides for meeting with Loren Frank

Issue - State: closed - Opened by edeno about 8 years ago

#20 - Should we include iCA1 when defining a ripple?

Issue - State: closed - Opened by edeno about 8 years ago - 3 comments

#19 - Scaling up analysis to process multiple days

Issue - State: closed - Opened by edeno about 8 years ago - 4 comments

#18 - Compute Gamma, Theta relative to ripples

Issue - State: closed - Opened by edeno about 8 years ago

#17 - Write test code for ripple segmenting and spectral functions

Issue - State: closed - Opened by edeno about 8 years ago

#16 - We should use their computed ripples in the spectral analysis for comparison

Issue - State: closed - Opened by edeno about 8 years ago

#15 - Email paper about group delay

Issue - State: closed - Opened by edeno about 8 years ago - 1 comment

#14 - Add speed criterion to ripple detection

Issue - State: closed - Opened by edeno about 8 years ago - 3 comments

#13 - Categorize ripple types

Issue - State: closed - Opened by edeno about 8 years ago - 2 comments

#12 - Examine phase locking pfc neurons to hippocampal theta

Issue - State: closed - Opened by edeno about 8 years ago - 1 comment

#11 - Compute Loeve spectrum to examine cross-frequency coupling

Issue - State: closed - Opened by edeno about 8 years ago

#10 - Compute peri-event time histogram of neurons relative to ripple event

Issue - State: open - Opened by edeno about 8 years ago

#9 - Compute ripple evoked response in PFC

Issue - State: closed - Opened by edeno about 8 years ago

#8 - Compute Group Delay

Issue - State: closed - Opened by edeno about 8 years ago

#7 - DIO pulses are corrupted for a couple of animals

Issue - State: open - Opened by edeno about 8 years ago - 2 comments

#6 - Quantify behavior

Issue - State: open - Opened by edeno about 8 years ago

#5 - Decide whether it is easier to use the Frank Lab Data Filter Framework or if it's easier to code in own format

Issue - State: closed - Opened by edeno about 8 years ago - 1 comment
Labels: question

#4 - Reproduce analysis from Jadhav paper

Issue - State: closed - Opened by edeno about 8 years ago - 3 comments

#3 - Unsure on how to find information about a single trial

Issue - State: closed - Opened by edeno about 8 years ago - 2 comments
Labels: question

#2 - Unsure how to find the trials within the epochs

Issue - State: closed - Opened by edeno about 8 years ago - 1 comment
Labels: question

#1 - Having trouble finding all the LFP recordings

Issue - State: closed - Opened by edeno about 8 years ago - 1 comment
Labels: question

GitHub / edeno/Jadhav-2016-Data-Analysis issues and pull requests