philipbjorge

from ij import IJ
from ij import WindowManager as wm
from ij import ImagePlus
import time

def open_file_dialogue(window_title="", path_restriction=None):
	"""
	Opens a file dialogue and returns the path to the chosen file.
	Returns None on an invalid file or dialogue cancellation (prints to log).
	window_title will appear in the file dialogue window title.

philipbjorge

#Pearson's Coefficient Range between -1 and 1. -1 is a negative correlation and +1 is a positive correlation.

Scatter plots and PCs point to colocalization especially where it is complete (Fig. 5A and B); however, they rarely discriminate differences between partial colocalization or exclusion, especially if images contain noise.

Overlap Coefficient

Mander's removes mean fluorescent intensity from Pearson's, which gives a new value between 0 and 1.0, where 1.0 is 100% colocalization.

philipbjorge

; Stupid simple autoit script for cleaning up "orphaned" notepad instances
; I end up with dozens of notepad instances after a day of coding and it's a pain to close all these manually
; as I do want to keep some of them.
; Public Domain
; Philip Bjorge
; June 2, 2012
Local $windows=WinList()

For $i = 1 To $windows[0][0]
   If StringInStr($windows[$i][0], "Notepad", 0) Then

philipbjorge

Zoomify Procedures

Imaging Computer

1. Navigate to the "C:\Images\Moths" directory.
2. Click and run the export_as_tiff.bat file. This will take a minute, but it will move any new tiffs to the "C:\Images\Moths\Final Moths Tiff" directory.
3. Open the program ZoomifyConvertor.exe in "C:\Images\Moths"
4. Navigate to the "C:\Images\Moths\Final Moths Tiff" and sort these by date, noticing which images are new.
5. Highlight the new images to be zoomified and drag them onto your already opened Zoomify window. This will create a set of folders (named after the tiffs) in the "C:\Images\Moths\Final Moths Tiff" directory.
6. When Zoomify is finished, select all these new zoomified folders and copy them onto a flash drive.
7. Then move these folders from "C:\Images\Moths\Final Moths Tiff" into "C:\Images\Moths\Final Moths Zoomified" (We want to keep things organized on the filesystem).

philipbjorge

#!/usr/bin/env python

import sys
import math
from random import shuffle
import numpy as np

loop_iters = 0
"""
NOTE: I'm pretty sure we're using the word bogo without knowing what it means...

philipbjorge

[1, 2, 3].collec {|i| i*2}
# => [2, 4, 6]
"hello world".capitalzie
# => Hello world

philipbjorge

class Counter
  attr_accessor :data
  def initialize(initial)
    @data = initial
  end
end

expected = [0, 1, 2, 0, 5]
actual = []

philipbjorge

import OpenGL.GL as GL
import OpenGL.GL.shaders
import ctypes
import pygame
import numpy

vertex_shader = """
#version 330

in vec4 position;

philipbjorge

__author__ = 'philipbjorge'
import sys, urllib, json, argparse, urllib2
from os import remove
from os.path import abspath, isdir, join, exists, getsize
from guessit import guess_episode_info
from collections import defaultdict
from sys import stderr
import fileDownloader

DEBUG = True

philipbjorge

console.log("apartment\taddress"); 
$.each($(".buildings li"), function(i, v) { 
  var apartmentName = $(v).children("h2").text();
  var apartmentAddress = $(v).find("strong").text();
  console.log(apartmentName + "\t" + apartmentAddress);
});