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import os | |
import glob | |
import json | |
import numpy as np | |
LABELS = { | |
'Tissue': 1, | |
'Tumor': 2 | |
} | |
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import argparse | |
import glob | |
import os | |
import h5py | |
import numpy as np | |
from natsort import natsorted | |
from tqdm import tqdm | |
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A collection of groovy and python (paquo) scripts used for image analysis in QuPath. |
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#!/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 |
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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 |