tsikup

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

tsikup

#!/bin/bash
set -e

usage="$(basename "$0") [-h] [-i PROJECT] [-v VM] [-p PYTHON] [-d NOTEBOOKS]
Make a user provide SSH key and jupyter notebooks (in roles/bootstrap/files/notebooks) to each user listed in var/common.yml
where:
    -h  show this help text
    -i  google cloud project id
    -v  name of instance/virtual machine
    -p  python path

tsikup

A collection of groovy and python (paquo) scripts used for image analysis in QuPath.

tsikup

import argparse
import glob
import os

import h5py
import numpy as np
from natsort import natsorted
from tqdm import tqdm

tsikup

import os
import glob
import json
import numpy as np

LABELS = {
  'Tissue': 1,
  'Tumor': 2
}