hirokai

run("Stack From List...", "open=/Users/hiroyuki/Desktop/bf.txt");
run("Z Project...", "projection=[Average Intensity]");
run("Calculator Plus", "i1=bf.txt i2=AVG_bf.txt operation=[Subtract: i2 = (i1-i2) x k1 + k2] k1=1 k2=0 create");

hirokai

# Used in combination with yes/no checker (http://hirokai.github.io/yesnochecker/)

list = [
	[0,[90]],
	[100,[22,25,38,39,40,43,45,46,52,53,54,55,56,59,62,68,69,70,71,72,73,74,75,76,77,79,80,81,85,86,87,89,90,93,94,95,96,97,98,99,100]],
	[200,[1,2,3,4,5,6,7,9,10,11,12,13,14,16,17,18,19,20,21,22,23,24,25,26,28,29,30,31,32,33,34,35,42,44,45,48,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,67,69,70,71,72,73,75,76,77,78,79,81,82,83,84,85,86,87,88,89,90,91,92,93,95,96,97,98,100]],
	[300,[4,6,10,11,12,13,15,17,18,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,56,57,58,59,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100]],
	[400,[1,3,4,5,6,9,10,11,12,13,15,16,17,18,19,25,26,29,30,31,32,33,34,35,36,37,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54]]
]

hirokai

import requests
import keyring
import json
import csv

gist_images = 'XXXX'
gist_rois = 'YYYY'

username = 'ZZZZ'
password = keyring.get_password('Github API', username)

hirokai

// Move to next slice, and reset scale, autocontrast, and make 250x250 rect.

run("Select None");
run("Next Slice [>]");
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
resetMinAndMax();
run("Enhance Contrast", "saturated=0.3");
run("Specify...", "width=250 height=250 x=256 y=256");

hirokai

import matplotlib.pyplot as plt
import csv
import numpy as np

ns = []
ms = []
with open('result.csv','rb') as f:
	reader = csv.reader(f)
	for row in reader:
		if not row[3].startswith('Fwd'):

hirokai

require 'kconv'
require 'mail'  # gem install mail
require 'csv'

def parse_message(message)
	m = Mail.new(message)
	o = {:id => m.message_id, :from => m.from, :to => m.to, :subject => m.subject, :reply => m.in_reply_to, :date => m.date, :ref => m.references}		
	p o
	o
end

hirokai

# Make time lapse of stitched image.
# Uses Numpy, Scipy, and tifffile

import numpy as np  # numpy
import tifffile  # tifffile
import cv2  # opencv
from scipy.ndimage.interpolation import zoom  # scipy
import json

original_side = 1024

hirokai

Basic

• Auto contrast (.ijm)
  • https://gist.github.com/hirokai/41308d05eafa86c967df

Intermediate

• Cropping files using file list and ROIs saved on Gist.

  • https://gist.github.com/hirokai/150178c8ae7bb8aca8dd

• Crop and merge images by ROIs (.py)

hirokai

def compute(i):
	import time,socket
	host = socket.gethostname()
	time.sleep(1)
	return (host, i)


def search():
	import fnmatch
	import os

hirokai

# 'compute' is distributed to each node running 'dispynode';
# runs on each processor in each of the nodes

from compute_simplest import compute,search

def main(n):
    import dispy
    import logging
    import time
    import numpy as np