Data for "Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10"
By Leonard Campanello, Maria Traver, Hari Shroff, Brian Schaefer, and Wolfgang Losert

This repository contains 4 directories:
1. Raw Image Data
2. Processed Image Data
3. Analyzed Image Data
4. Simulations Data

1. Raw Image Data: 
- Contains the raw iSIM image data described in the manuscript
- The directory called "20 min" contains the images taken 20 min post activation
- The directory called "40 min" contains the images taken 40 min post activation

2. Processed Image Data
- Contains processed images for each cell in each of the iSIM images in "Raw Image Data"
- The description of each file contained is as follows:
	a. "RoughMask.tif" is the manually annotated mask that should be applied to the raw image
	b. "Channel1_binary.tif" is the segmented objects obtained from processing channel 1 of the raw data within "RoughMask.tif"
	c. "Channel2_binary.tif" is the segmented objects obtained from processing channel 2 of the raw data within "RoughMask.tif"
	d. "CellMask.tif" is the cell boundary that was calculated from processing channels 1 and 2 of the raw data within "RoughMask.tif"
	e. "Channel2_skeleton.tif" is the medial-axis skeletons of the binary objects in "Channel2_binary.tif"

3. Analyzed Imaged Data
- Contains results from the analysis of the data in "Processed Image Data"
- The description of each file contained is as follows:
	a. "FilamentLengths.csv" are the lengths in microns of each Bcl10 structure in the corresponding processed image as per the skeleton in "Channel2_skeleton.tif". Values of -1 are puncta.
	b. "ContactEdgeDistances.csv" and "ContactEdgeDistanceWeights.csv": Each row represents a SINGLE Bcl10-autophagosome contact (i.e., the overlay between "Channel1_binary.tif" and "Channel2_binary.tif"). The overlapping voxels may span multiple edge-distance regions along the Bcl10 structure; thus, each edge-distance value and the corresponding weight of that value (i.e. the relative number of voxels in the region) were recorded.

4. Simulations Data
- Contains the results from the simulations described in the manuscript
- The folders with prefix "20_" contain the results for each of the 1000 simulations performed with the parameters described in the folder name
- The folder name breakdown is as follows:
	a. attach_pBefore= pAttach in the manuscript
	b. carma1_pActivate= pActivate in the manuscript
	c. Degrade Meth 0 is when there is no degradation (used in Figure 4 of the manuscript)
	d. Degrade Meth 2 is when there is degradation (used in Figure 5 of the manuscript)
	   In such cases, pDegrade= pDegrade in the manuscript
- For example, folder "20_attach_pBefore=0.001_carma1_pActivate=0.010_Degrade Meth 2_Degrade pDegrade=0.01" is
	pAttach = 0.001
	pActivate = 0.01
	pDegrade = 0.01
- Within each folder are files with prefixes "DataMovie2_" which contain the raw simulations data
- The file name breakdown is as follows:
	a. bclInitLevel= is the number of Bcl10 monomers initialized in the simulation
	b. carma1InitLevel= the number of nucleation sites initialized in the simulation
	c. degradeMethod= is the degradation method (either 0 for no degradation, or 2 for with degradation)
	d. _vN where N = the Nth iteration of the simulations with the same initial condition
- For example, file "DataMovie2_bclInitLevel=9085_carmaInitLevel=22_degradeMethod=2_v5" is
	initial number of Bcl10 monomers = 9085
	number of nucleation sites = 22
	with degradation
	the 5th repeat of the simulation with those initial conditions