Data and analysis code for "Olfactory nerve transection transiently activates olfactory ensheathing cells in Xenopus laevis larvae"

Abstract

This repository contains data and Python scripts that were used to quantify and analyze phosphorylated rpS6 (Ribosomal protein S6) signal in the olfactory nerve of larval Xenopus laevis. Phosphorylated rpS6 was immunohistochemically labeled in tissue containing the olfactory nerve and olfactory bulb. Multiphoton microscopy was used to visualize the signal as 3-dimensional image stacks. Two image stacks were acquired for each animal. In one, the olfactory nerve was transected; the other side served as uninjured control. All samples were measured at different time points after olfactory nerve transection.

The dataset comprises of the original image data, experiment metadata, a notebook with the analysis workflow, and results of calculations performed with the Python scripts.

data.zip: Uncompressed archive of original image stacks. All original imaging data are in Nikon nd2-format. Different time points after olfactory nerve transection are sorted in subfolders.

cropping_range.csv: Database of range values to reduce the image size in y-dimension. For each filename, ycutoff_begin and ycutoff_end are provided in pixels on the y-axis. The area inside the begin and end pixel index is included in the analysis.

rps6_code.py: Script collection to process the image stacks.

environment.yml: Modules used in the python environment. Can be used to recreate the analysis environment with conda.

OEC_rpS6_analysis.ipynb: Jupyter notebook with the workflow of analysis, statistics and figure creation.

rps6_ON_cropped_gaussianbg35_median3_cumsum.csv: Database of preprocessed data. Columns: name indicates original image stack file name, time after transection indicates sample group according to time after olfactory nerve injury, animal indicates a reference number for specimen of the same day of microscopy, OB side indicates which hemisphere was visualized (nts, not-transected; ts, transected), cumulative rpS6 235/236 intensity gives the sum of the pixel intensities of the image stack after preprocessing.