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Macrophage Analysis Wiki

This is a short overview on the scripts used for analyse spatial patterns of macrophage distributions. The analysis tools are implemented in Python 3.6, the following Python modules need to be installed:

• numpy
• scipy
• pandas
• seaborn
• matplotlib
• skimage
• json
• argparse

Usage

The workflow is shown in the diagram above. As input the following files need to be provided.

Metafile

mouse_name	type	analysis_file_vessels	analysis_file_macrophages	x_resolution [um]	y_resolution [um]	vessel_channel	macrophage_channel
mouse_1	4 weeks	vessel_file1.tif	macrophages_1.csv	400	400	0	1
mouse_1	4 weeks	vessel_file2.tif	macrophages_2.csv	400	400	0	1
mouse_2	2 weeks	vessel_file3.tif	macrophages_3.csv	300	300	1	0

Series of vessel images

Binary images containing segemented vessels

X-Y positions of macrophages

	X	Y
1	225	37
2	186	220
3	160	279

Parameter file

The parameter file has the following content

    "data_directory": "/directory/to/your/data/",
    "output_directory": "/directory/to/your/output/",
    "meta_data_file" : "meta_file",
    "subfolder_vessel_images" : "subfolder/",
    "type_column" : "tumor_type",
    "macrophage_channel"  : ["macrophage_channel1", "macrophage_channel2"],
    "macrophage_position_files"   : ["macrophage_channel1_files","macrophage_channel2_files"],  
    "selected_feature" : ["distance_vessels"],
    "occupancy_radius" : 10.0,
    "occupancy_sampling" : 10000

The default parameter file needs to be adjusted according to the local environment and column names of the input key-file.

Features

The following features can be calculated

1. nearest distance of macrophages to the vessels
2. nearest distance of macrophages to thick vessels (here thick is defined by a threshold on the vessel area)
3. nearest distance of macrophages to thin vessels (here thin is defined by a threshold on the vessel area)
4. normalized distance of macrophages to the vessels (here the distances are normalized to the distances that would stem from a completely random distribution)
5. occupancy of vessels
6. n-nearest neighbor distances among macrophages

Acknowledgements