Run the script 'sh run_script.sh $brainID' get the results.
Code Repo for the paper :
Sukhendu Das, Jaikishan Jayakumar, Samik Banerjee, Janani Ramaswamy, Venu Vangala, Keerthi Ram, and Partha Mitra.
BioRxiv (2019): 252247.
Store the input Brain images in JP2 format with the alphabet F (to represent fluoroscent section) within the name in a folder with the brainID.
If you have Brain Region Segmentation (as .mat files) store that in the folder $brainID/reg_high_seg_pad/
If you have Brain Region Segmentation in other format, read the segmenation appropiately so that it represents a single-channel image in line 28 of GFP_Cell_Detection/main_bam.m
If you donot have Brain Region Segmentation, comment out line 28 of GFP_Cell_Detection/main_bam.m and add a line to create a white single-channel image of the same size as your input image.
The output is in GeoJSON format with the center locations marked as (y, -x) correponding to the (x,y) co-ordinate in the corresponding image
The names of the input image, Brain region segmentation map, output GeoJson will be the same as the input image, with same/different extensions.