Zewen Kelvin Tuong zktuong
zktuong
/ Batch Counting IHC.ijm
Created
August 22, 2017 02:04
— forked from eeelinn/Batch Counting IHC.ijm
ImageJ macro that semi-automatically counts multiple DAB positively stained nuclei samples from IHC experiments in a batch. Influenced by: https://gist.github.com/zktuong/2b281aed13a089abb1de2b03a177754d
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| //NOTE: Before counting, please go to Analyze>>Set Scale and set the scale for image in pixels/um. Check "global" to maintain the same scale for all the images. | |
| input = getDirectory("Input directory"); //Folder with images you want counted | |
| output = getDirectory("Output directory"); //Folder where you want to save the new data (saves image of positive and total cells each) | |
| keyword = "5HT"; //Keyword in the file names that you want (in case there are other photos in the folder) | |
| suffix = ".tif"; //Works with tiff images | |
| processFolder(input); | |
| waitForUser("Batch Completed", "Batch Counting IHC has finished. Thank you for using!"); |
zktuong
/ VarScan2_format_converter_oncotator converter.py
Last active
April 4, 2017 00:34
— forked from PoisonAlien/VarScan2_format_converter.py
NativeToVcf() creates a vcf file that oncotator can use as input. As before, the script will auto detect the input format (native or vcf). Only goes one way at the moment: Standard VarScan2 VCF output -> Standard VarScan2 native output -> oncotator-friendly VCF
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| __author__ = "Anand M, edited to be a oncotator input friendly version by ZK Tuong" | |
| ''' | |
| Takes output file generated by VarScan2 somatic programme and converts the formats. | |
| ''' | |
| import argparse, math, re | |
| parser = argparse.ArgumentParser( | |
| description="Converts VarScan2 somatic vcf to native format and vice-versa.\nInput is automatically detected") |