Create README.md

README.md

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+The following Matlab scripts were developed to analyze light microscopy data, calculate fibril persistence length and quantify ER membrane curvature measurements.
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+Bäuerlein FJB et al. (2017) Cell
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+
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+# ER_mobility_analysis_part1.m
+# ER_mobility_analysis_part2.m
+# ER_mobility_analysis_part3.m
+
+Matlab script in three parts to calculate the accumulation and variance of the endoplasmic reticulum around inclusion bodies (IB).
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+	•	part 1: loads all ER-movies, identifies individual IBs, defines IB boarders and creates FIJI script for bleach correction
+	•	run FIJI script for bleach correction of the ER-movies before continuing with part2
+	•	part 2: calculates ER-variance, defines extracellular and nuclear regions to exclude from averaging, calculates rotational averages and saves analyses to output files
+	•	part 3: cohort analysis for all IBs found and plotting of radial averages of ER and IB signal plus ER variance 
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+Necessary data: 
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+	1)	single exposure in the GFP-channel to identify Htt-GFP inclusion bodies 
+	2)	10Hz time series of the ER-channel over 20-30s
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+
+
+# RSDA.m
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+Ring Shape Detection Algorithm (RSDA).
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+This Matlab script analyses light microscopy data acquired with the FEI CorrSight microscope using the MAPS-Software:
+the script analyses the EM-grid overview taken with x times y tiles, identifies inclusion bodies by detecting ringlike structures that are formed by mCherryUb around the IB and marks the detected IBs in the bright field micrographs by a surrounding rectangle. Finally an Excel list is written, with location, morphological properties, the distance of IBs to the grid bars and a quality score to optimize the selection for FIB lamella preparation.
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+
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+# Persistencelength_full.m
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+This Matlab script was developed to calculate the persistence length of fibrils traced in cryo-EM data with Amira 6.0.1, using the XTracing module.
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+Needed data is the „Attribute“ dataset derived from the XTracing module saved as .xml file. After manually transforming to .xls format, the data is first transformed by the Persistencelength_full.m script with the Amira_lineset_conversion.m script (see below) and by scripts previously developed by M. Jasnin & E. Villa (Jasnin et al. (2013) PNAS) to space the datapoint equidistantly and following the persistence length is calculated with the core script Persistencelength.m.
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+
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+# Persistencelength.m
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+This Matlab script is the core of the Persistencelength_full.m script and performes the actual calculation of the persistence length of fibrils.
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+
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+# Amira_lineset_conversion.m
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+Matlab script, that aggregates data from the Amira 6.0.1 file.
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