Figure 4 - Source data 1:

This folder contains the quantification results used as source data for Figure 4 A-E. 

In brief, we used binary segmentation masks derived from the probabilistic softmax output of the trained models for each image to quantify the number and the mean intensity of cFOS-positive ROIs in a selected area (e.g. stratum pyramidale of CA1).

The analyses were performed with the code provided in the Jupyter Notebook "fig_3_4_quantification.ipynb" in our GitHub repository: 

https://github.com/matjesg/bioimage_analysis/blob/master/notebooks/fig_3_4_quantification.ipynb

Method details are provided in the Material & Methods section of our paper.
____________________________________________

Additional file descriptions:


ROIs_wue1.csv:

Contains the raw data of the ROI quantifications: 
 - mean_intensity: 	mean cFOS signal intensity of individual ROI
 - label: 		ID of annotated cFOS-positive ROI
 - area:		area of individual ROI in pixel
 - Nummer:		ID of analyzed image
 - region area:		area of analyzed region in pixel (e.g. stratum pyramidale in CA1)
 - model, unet, ens:	identification of model / ensemble used for analysis
 - subarea:		analyzed region (CA1, CA3, DG, DG_infra, or DG_supra)
 - init:		type of initialization (only from-scratch for Lab-Wue1)


quantifications_wue1.csv:

Data of "ROIs_wue1.csv" further processed to ultimately calculate for each image ("Nummer" = image id) the normalized number of cFOS-positive ROIs per analyzed area ("norm_cfos_per_area") and the normalized mean cFOS signal intensity ("norm_mean_intensity"). This file also contains information about treatment condition ("Kondition"; H: homecage, -: context only, +: context conditioned), analyzed hippocampal subregion ("subarea"), and the model or ensemble that was used for the respective analysis ("ens", "unet", "model", "init"). 



stat_results_quantifications_wue1.xlsx:

Results of all individual statistical analyses of "quantifications_wue1.csv", including calculated effect sizes (eta^2) that are plotted in Figure 4A-E. Individual tabs indicate the respective analysis, e.g. "CA1-#cFOS+ nuclei".
 - 1: group 1, homecage controls (H)
 - 2: group 2, context controls (C-)
 - 3: group 3, context conditioned (C+)
 - anova_ok: Indicates whether the pre-requisites for parametrical testing (normal distribution and euqality of variances) were met (True), or not (False). 
 - H_kwa_all: H-statistic of Kruskal-Wallis-ANOVA between all three groups
 - U_mwu: U-statistic of Mann-Whitney-U test between indicated groups, e.g.: mwu1_vs_2 - Mann-Whitney-U test between group 1 (H) and group 2 (C-)
 - eta^2_*: eta-squared of indicated test
 - p_*: p-value of indicated test
 - c_*: critical eta-squared of indicated test at p = 0.05
 - c0.01_*: critical eta-squared of indicated test at p = 0.01
 - c0.001_*: critical eta-squared of indicated test at p = 0.001