rmd13

Collections of scripts harvested mainly from Pete, but also picked up from the forums

TOC

Accessing dynamic measurements.groovy - Most annotation measurements are dynamically created when you click on the annotation, and 
are not accessible through the standard getMeasurement function. This is a way around that.

Affine transformation.groovy - access more accurate measurements for the affine transformation used in the image alignment (m5/m6+)

Alignment of local cells.groovy - check neighborhood for similarly aligned cells

rmd13

from hashlib import md5
from sqlite3 import connect as sql_conn
from time import localtime, strftime


class IllegalException(Exception):
    def __init__(self, *args):
        super().__init__(*args)

rmd13

/**
 * A basic GUI to help monitor memory usage in QuPath.
 *
 * This helps both to find & address out-of-memory troubles by
 *   1. Showing how much memory is in use over time
 *   2. Giving a button to clear the tile cache - which can be
 *      using up precious memory
 *   3. Giving quick access to control the number of threads used
 *      for parallel processing
 *

rmd13

% Clean start!
clear all, clc

%% Parameters
% Path to input file
videoPath = '..\..\leap\data\examples\072212_163153.clip.mp4';

% Path to output file
% savePath = '..\..\leap\data\examples\072212_163153.clip.h5';
savePath = 'C:\tmp\072212_163153.clip.h5';

rmd13

% Example of looping through a folder to process a series of images. 
% In this case, perform channel math.

% For convenience, this example uses EasyXT, but feel free to adapt it as needed.
% Get EasyXT Here: http://lacan.github.io/EasyXT/
% The ChannelMath method is borrowed from the XTension with the same name, made by Bitplane.

folder_name = uigetdir();
listing = dir(folder_name);