Microscale spatial fragmentation promotes bacterial survival under antibiotics

Dataset associated with: Benbenisti et al 2026 "Microscale spatial fragmentation promotes bacterial survival under antibiotics"PROJECT README: DATA REPOSITORY METADATAThis document provides an overview of the folder structure and explains the meaning of key columns in the CSV data files within this repository.--------------------------------------------------1. FOLDER STRUCTURE--------------------------------------------------The repository is organized by experimental condition, with subfolders for the different stages of image/data processing:data repo/|+-- Amp/ (Ampicillin Experiment Data)| +-- droplets data/ (Raw ImageJ segmentation ROIs)| +-- merged data/ (Count data merged with volume metadata)|+-- Gen/ (General/Control Experiment Data)| +-- bac data/ (Raw bacterial count data per droplet)| +-- droplets data/ (Raw ImageJ segmentation ROIs)| +-- merged data/ (Count data merged with volume metadata)|+-- Poly B/ (Polymyxin B Experiment Data)| +-- droplets data/| +-- merged data/|+-- densyl Poly B/ (Densyl-labeled Polymyxin B Data)| +-- bac data/ (Bacterium-level intensity data)| +-- droplets data/| +-- merged data/ (Merged volume and bacterium intensity data)|+-- Bocillin FL/ (Bocillin-FL Experiment Data)| +-- merged data/ (Final merged data, including intensity ratios)|+-- py scripts/ (Python Analysis Scripts) +-- data analysis/ (Post-processing and plotting scripts) +-- image analysis scripts/ (Image processing, stitching, and quantification scripts) +-- Model simulation script--------------------------------------------------2. CSV COLUMN DEFINITIONS--------------------------------------------------A. Droplet Segmentation Files (e.g., droplets data/C*.csv)Column Name | Meaning------------|----------------------------------------------------Label | Unique identifier for the segmented droplet/ROIArea | Area of the segmented droplet (units depend on scale)X | X-coordinate of the droplet centroidY | Y-coordinate of the droplet centroidPerim. | Perimeter of the segmented droplet (may only be in some files)B. Bacterial Count Files (e.g., bac data/bacteria_countsC*.csv)Column Name | Meaning---------------|----------------------------------------------------Chip | The name of the microfluidic chip (e.g., C8, C7)Hour | Time point of measurement (e.g., 0, 3, 5)Droplet | Unique droplet identifier (matches 'Label' in droplet files)Bacteria Count | Total number of bacteria detected inside the dropletC. Merged Data Files (e.g., merged data/merged_bacteria_countsC*.csv)Column Name | Meaning-------------|----------------------------------------------------Slice | Full sample condition identifier (e.g., C1 - Control)Count | Number of bacteria found in the dropletDroplet | Droplet IDArea | Droplet area (processed value)Volume | Calculated volume of the droplet (micrometers cubed)log_Volume | Log base 10 of the droplet volumeBins_vol_txt | Categorical bin for droplet volume sizeWell | Experimental well/chamber nameinitialOD | Initial Optical Density of the bacterial cultureD. Intensity/Final Data Files (e.g., densyl Poly B/merged data/*.csv)Column Name | Meaning-----------------------|----------------------------------------------------Bacterium | Unique identifier for an individual bacteriumMean_Top25_Intensity | Mean fluorescence intensity of the top 25 brightest pixels in the bacterium ROIGFP intesity | Overall GFP fluorescence intensity measurementintesity ratio | Calculated ratio (e.g., fluorescence / biomass) for quantitative analysis