Working Memory Ablation: Density Maps

This repository contains MATLAB scripts for visualizing ablated cell data. The pipeline calculates ablated voxels, merges datasets across subjects, and generates density map visualizations.

Pipeline Overview

The analysis is split into two main workflows. Scripts should be executed in the exact order listed below.

Part 1: Cell Counting and Plotting

1. CountAblatedCells_Script.m

   • Description: Counts the number of voxels in the ablated region for each subject.
   • Outputs: A .csv file for each fish containing the voxel counts.
     • Two binary .tif files corresponding to the areas of interest (pre- and post-ablation).

2. mergeCSV.m

   • Description: Scans each fish folder and merges all individual .csv files into a single .csv file.

3. makeplots.m

   • Description: Visualizes the voxel data before and after ablation. Generates plots for all fish aggregated together, as well as separate plots for individual fish.

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Part 2: Density Maps and Visualization

1. IdentifyAblation.m

   • Description: Makes a density map for the targeted ablation area.

2. heatmap.m

   • Description: Processes the density map data to render a heatmap, allowing for a better visual display of the ablation distribution.