Dominik Lindner dominikl

	Dataset:name:Mouse_HE	/uod/idr/filesets/idr0154-queen-hdbr/851 2 RBP1 KO P1 T Sectioned head to tail 11.tif
	Dataset:name:Mouse_HE	/uod/idr/filesets/idr0154-queen-hdbr/872 2 RBP1 KO 15.5 T Sectioned tail to head 5.tif
	Dataset:name:RNAscope	/uod/idr/filesets/idr0154-queen-hdbr/1268_CS16_11_MXRA5-Change Scaling-04.ome.tiff

	import os
	os.environ["ZARR_V3_EXPERIMENTAL_API"] = "1"

	import zarr
	import argparse


	parser = argparse.ArgumentParser(description="Convert ome.zarr from zarr spec 2 to 3")
	parser.add_argument("input", help="The input zarr")
	parser.add_argument("output", nargs="?", help="Optional output zarr")

	import re
	import subprocess
	from experimental import Plate, Image, create_companion
	# https://github.com/ome/ome-model/blob/master/ome_model/experimental.py
	# (pip install ome-model)

	# R44821_160620150002i3t001A06f01d2.ome.tif
	pat = re.compile(r"^(?P<plate>.?)i3t(?P<timepoint>\d+)(?P<wellrow>\w)(?P<wellcol>\d{2,})f(?P<field>\d{2})d(?P<channel>\d)\.")
	plate_name = "R44821_160620150002"
	order = "XYCZT"

	import matplotlib.pyplot as plt
	import numpy as np
	import omero
	from omero.gateway import BlitzGateway, ColorHolder
	from omero.model import MaskI, RoiI
	from omero.rtypes import rdouble, rint, rstring
	from skimage.filters import threshold_otsu
	from skimage.measure import label, regionprops

	OME_HOST = "merge-ci"

	import omero.api.IQueryPrx;
	import omero.gateway.Gateway;
	import omero.gateway.LoginCredentials;
	import omero.gateway.SecurityContext;
	import omero.gateway.model.ExperimenterData;
	import omero.gateway.model.FilesetData;
	import omero.log.SimpleLogger;
	import omero.model.Fileset;
	import omero.sys.ParametersI;