dominikl

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")

dominikl

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"

dominikl

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"

dominikl

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;