Workflow

• Obtain real dataset.

• Create 3D visualization plots (jupyter notebook) and 2D density plots (MatLab) based on real dataset.

• Sample selection (MatLab) based on real dataset.

• Obtain generated dataset.

• Create 3D visualization plots (jupyter notebook) and 2D density plots (MatLab) based on generated dataset.

• Compare the visualization results between real dataset and generated dataset and analyze the similarity between them.

1 Dataset: PAINT_DiffTemp

The shapes of microgels respond to the stimulation of temperatures. Check the features in the paper:

Microgel PAINT – nanoscopic polarity imaging of adaptive microgels without covalent labelling

1.1 Dataset

Collected real dataset

.\Microgel\4_Microgel_plotter_V1_density\PAINT_DiffTemp\Core-shell\*C\Microgel_plotter_v2_solvatochromism\

where "*C" means the dataset for the samples at temperature ${\ast }^{\circ }C$

Generated dataset

.\Microgel\4_Microgel_plotter_V1_density\results_mtemp\results_mtemp_hilo

Notes:

• "sample_go1.ply" denotes the original real sample 1

• "sample_gg1.ply" refers to the corresponding generated sample 1.

• "sample_info1.ply" includes the information for normalizing "sample_go1.ply" and "sample_gg1.ply"

1.2 Matlab files

Generate the 2d density for generated "go" "gg" samples:

.\Microgel\4_Microgel_plotter_V1_density\visualize_hilo_density.m

Rank the correlation values to select the samples:

.\Microgel\4_Microgel_plotter_V1_density\SampleSelection.m

2 Dataset: 24

There are four different states of surface of microgels, check the details in the paper

Deformation of Microgels at Solid–Liquid Interfaces Visualized in Three-Dimension | Nano Letters

3 Dataset: 16FM

Microgel point cloud in 2d coordinate with lifetime values as the third dimension.

Dataset folders

Collected real dataset:

.\Microgel\16-FM\lifetime

Generated dataset:

.\Microgel\16-FM\results_lifetime

Notes:

• "sample_go1.ply" denotes the original real sample 1

• "sample_gg1.ply" refers to the corresponding generated sample 1.

• "sample_info1.ply" includes the information for normalizing "sample_go1.ply" and "sample_gg1.ply"

Matlab files

Extract the samples from the entire slide and create 2d density plot for collected real data:

.\Microgel\16-FM\pc16fm_real.m

Create 2d density plot for "go""gg" files

.\Microgel\16-FM\pc16fm_gogg.m

Jupyter Notebooks

.\Microgel\jupyter_notes

• main_project_real_data_007.ipynb

  This notebook includes functions such as convex hull calculation, histogram calculation, visualization, etc.

• Fancy_16FM.ipynb:

  Generates fancy visualization of 3d point cloud for 16FM dataset

• Fancy_point_cloud.ipynb:

  Generate fancy visualization of 3d point cloud for PAINT_DiffTemp dataset

• Fancy_real_data_selection.ipynb:

  Generated 3D visualization for the selected point clouds according to the sample selection information.

• Sample_selection.ipynb:

  Present the density png plots from the MatLab-generated density folder.

• 2d_project_3d_visual.ipynb

  Generates 2d projection and 3d scatter plot of microgel samples.