CNMF-E eLife submission

This repo supports our submission of CNMF-E work to eLife. All the code and data are shared for reproducible research. The figures and the videos shown in our paper can be automatically generated using the provided code. The latex file for writing the paper was provided as well. In a nutshell, you can completely reproduce our paper using this repo.

Author

Pengcheng Zhou, Columbia University, zhoupc1988@gmail.com

All rights reserved!

Requirements

1. MATLAB
2. pdfLatex
3. ffmpeg or other avi2mp4 converters

Folder descriptions

• main.tex & vancouver-elife.bst & references.bib (latex file & the eLife template & references)

  The manuscript can be generated by compiling main.tex

• ./code (all scripts and packages used in this project)

  • ./scripts_figures (scripts for generating all figure panels)

    • ./fig_intro (Figure 1 )
    • ./fig_bg (Figure 1E & Figure 2))
    • ./fig_initialization (Figure 3)
    • ./fig_sim (Figure 4)
    • ./fig_corr (Figure 5)

  • ./CNMF-E (CNMF-E package (12/02/2017))

  • ./CellSort (** PCA/ICA package **)

  • ./cbrewer (generate some fancy colormaps)

• ./data =

  ** since data files are too large for including them into github. you have to download them by yourself. Click here for downloading the data**

  • ./blood_vessel_10Hz.mat (Figure 6 )

    collected by Shay Q. Neufeld & Bernardo L. Sabatini at Harvard University)

    ./PFC4_15Hz.mat (Figure 7) ) collected by Shanna L. Resendez and Garret D. Stuber at University of North Carolina at Chapel Hill

  • ./bma22_epm_motioncorrected_round1_cropped_correction.mat (Figure 8)

    collected by Jessica C. Jimenez, Mazen A. Kheirbek & Rene Hen at Columbia University

  • ./CAMKII120_160317shock.mat (Figure 9)

    collected by Jose Rodriguez-Romaguera and Garret D. Stuber at University of North Carolina at Chapel Hill)

• ./Figs

  • ./Fig_introduction.tex (Figure 1)
  • ./Fig_BG.tex (Figure 2)
  • ./Fig_INIT.tex (** Figure 3 **)
  • ./Fig_SIM_part1.tex (Figure 4)
    • ./Fig_SIM_part2.tex (Figure 5)
  • ./Fig_Striatum.tex (Figure 6)
  • ./Fig_PFC.tex (Figure 7)
  • ./Fig_HIPPOCAMPUS.tex (Figure 8)
  • ./Fig_BNST.tex (Figure 9)

• ./Video

• ./results

Guide

We used two steps for generating paper figures:

1. generate all figure panels and videos using MATLAB. Figure panels are saved into each subfolder of ./Figs; videos are saved into folder ./Videos

2. create paper figures by combining all panels using the picture package in latex.

We tested these code under Ubuntu 16.04. The MATLAB version is R2015a. The commands for compiling tex file should work for both unix and linux systems. I haven't tested the Windows system, but it should be the same as compiling other latex files.

Figure 1 & Figure 2

MATLAB

>> run ./code/scripts_figures/fig_intro/main.m 
>> run ./code/scripts_figures/fig_bg/main.m

Latex

pdflatex ./Figs/Fig_introduction.tex
pdflatex ./Figs/Fig_BG.tex 

Results:

• Figure 1: ./Fig_introduction.pdf
• Figure 2: ./Fig_BG.pdf
• S1 Video: ./Videos/example_microendoscopic_data.avi
• S2 Video: ./Videos/background_comparison.avi

Figure 3

MATLAB

>> run ./code/scripts_figures/fig_initialization/main.m 

Latex

pdflatex ./Figs/Fig_INIT.tex

Results: Figure 3: ./Figs/Fig_INIT.pdf S3 Video: ./Videos/sim_initialization.avi

Figure 4

MATLAB

>> run ./code/scripts_figures/fig_sim/main.m 

Latex

pdflatex ./Figs/Fig_SIM_part1.tex

Results: Figure 4: ./Figs/Fig_SIM_part1.pdf S4 Video: ./Videos/sim_snr1_decompose.avi S5 Video: ./Videos/sim_snr6_decompose.avi

Figure 5

MATLAB

>> run ./code/scripts_figures/fig_corr/main.m 

Latex

pdflatex ./Figs/Fig_SIM_part2.tex

Results: Figure 5: ./Figs/Fig_SIM_part2.pdf

Figure 6

MATLAB

>> run ./code/scripts_figures/fig_striatum/main.m 

Latex

pdflatex ./Figs/Fig_Striatum.tex

Results: Figure 6: ./Figs/Fig_Striatum.pdf S6 Video: ./Videos/striatum_decompose.avi

Figure 7

MATLAB

>> run ./code/scripts_figures/fig_PFC/main.m 

Latex

pdflatex ./Figs/Fig_PFC.tex

Results: Figure 6: ./Figs/Fig_PFC.pdf S7 Video: ./Videos/PFC_decompose.avi

Figure 8

MATLAB

>> run ./code/scripts_figures/fig_hippocampus/main.m 

Latex

pdflatex ./Figs/Fig_HIPPOCAMPUS.tex

Results: Figure 8: ./Figs/Fig_HIPPOCAMPUS.pdf S9 Video: ./Videos/HIPPOCAMPUS_decompose.avi S10 Video: ./Videos/intervention.avi

Figure 9

MATLAB

>> run ./code/scripts_figures/fig_bnst/main.m 

Latex

pdflatex ./Figs/Fig_BNST.tex

Results: Figure 9: ./Figs/Fig_BNST.pdf S11 Video: ./Videos/BNST_decompose.avi

Figure 10

Figure 10 is a figure for illustrative purpose. I created the figure in an interactive way. Thus, I don't have the script for creating this figure.

Convert all avi movies to mp4 videos

All exported Videos from MATLAB are avi files. We used ffmpeg to convert them into mp4 format and rename as 'S* Video.mp4'

bash ./Videos/avi2mp4.sh
bash ./Videos/rename_videos.sh 

Compile the manuscript

Latex

pdflatex CNMF_E_final.tex
bibtex CNMF_E_final.tex
pdflatex CNMF_E_final.tex
pdflatex CNMF_E_final.tex

Results:

The paper: 📎CNMF_E_final.pdf

😃