johntmorgan / stereo_investigator_nucleator_bin Goto Github PK

This Python script produces binned nucleator data from Stereo Investigator outputs.
You can select any number of markers, any bin sizes, and any inquiry length you want.
You can investigate either area or volume. 
The comment sections below cover Python setup, file preparation, and variable sets.

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Section 1: setting up your computer to run this program
This program is written in Python 2.7.

Step 1: Install Python 2.7.3 from here: http://www.python.org/download/releases/2.7.3/
On the page, select the Windows MSI installer (x86 if you have 32-bit Windows installed,
x86-64 if you have 64-bit Windows installed.)
I suggest using the default option, which will install Python to c:/Python27

Step 2: Copy this program into the c:/Python27 directory
You can also put it into another directory that is added to the correct PATH.

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Section 2: file preparation for this program

Step 1: Create input files
Stereo Investigator doesn't mark nucleator data by region, but you can sort by modified 
Select all of the nucleator data for a region in the "display probe run list"
For each of your markers, highlight the marker, select "copy to clipboard"
Paste the data into an Excel spreadsheet. 
Save the spreadsheet a as tab delimited .txt file
Save the file using the naming convention "casename region celltype.txt"
If you have multiple runs to track (e.g., for reliability) save as "casename run region celltype.txt"
(Don't mess around with the headers, this program expects default Stereo Investigator output)

Step 2 (Optional):
This program can return either raw binned data, or data corrected by estimated cell number
To correct data by cell number, create an excel file with the format:
Column 1: Case
Column 2: Run number (or leave blank)
Column 3: Region name
Column 4: Cell marker name
Column 5: Number of cells

Save the file as a tab-delimited text file.

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