hirokai

def rgb2gray(rgb):
	r, g, b = rgb[0,:,:], rgb[1,:,:], rgb[2,:,:]
	gray = 0.2989 * r + 0.5870 * g + 0.1140 * b
	return gray


def compute(img):
	try:
#		print('Computing...')
		import time, socket

hirokai

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

from compute import compute,search,rgb2gray

def main(n):
    import dispy, random
    import logging
    import tifffile as tiff
    import time

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

hirokai

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


def search():
	import fnmatch
	import os

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

# 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

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

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

// 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 requests
import keyring
import json
import csv

gist_images = 'XXXX'
gist_rois = 'YYYY'

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