Merge channels and save as OME-TIFF using pyvips.

Merge-Channels-PyVips.py

# -*- coding: utf-8 -*-
"""
Created on Fri Nov 19 14:45:08 2021

@author: Ajay Zalavadia ([email protected])_
"""
import math
import os
import glob
import logging
from tqdm import tqdm

logging.basicConfig(level=logging.WARN) #change to INFO for more details
# Add vips binaries to path
vipshome = 'c:\\apps\\vips-dev-8.14\\bin'
os.environ['PATH'] = vipshome + ';' + os.environ['PATH']
import pyvips 
logging.info("vips version: " + str(pyvips.version(0))+"."+str(pyvips.version(1))+"."+str(pyvips.version(2)))

imagedir = 'D:\\input'
outputdir = imagedir #change this to save to a different folder

dataSets = glob.glob1(imagedir, '*_ch00.tif')

def eval_cb(image, progress):
        pbar_filesave.update(progress.percent - pbar_filesave.n)


for idx, dataset in enumerate(dataSets):
    str1 = dataset.split("_ch00.tif", 2)
    #print("Processing: "+ str1[0] + " " + str(idx) + " out of " + str(len(dataSets)))
    imagePrefix = str1[0]
    imageFiles = glob.glob(imagedir+'/'+imagePrefix+'_ch*.tif')

    outfilename = imagePrefix + '.ome.tif'
    outfile = os.path.join(outputdir, outfilename)
    pbar_filesave = tqdm(total=100, unit="Percent", desc=outfilename, position=0, leave=True)

    images = [pyvips.Image.new_from_file(os.path.join(imagedir, filename), access="sequential") for filename in imageFiles]

    out = pyvips.Image.arrayjoin(images, across=1)
    out = out.copy()
    out.set_type(pyvips.GValue.gint_type, "page-height", images[0].height)

    # Parameters for OME metadata
    width = images[0].width
    height = images[0].height

    # Need to handle more data types
    data_type = "uint8"
    if (images[0].interpretation=="grey16"):
        data_type = "uint16"
        
    bands = int(out.height/images[0].height)
    CalibrationX = 1000/float(out.xres) #Or out.xres
    CalibrationY = 1000/float(out.yres) #Or out.yres
    CalibrationUnits = "µm" #Or out.get("resolution-unit")
    
    # build minimal OME metadata
    metadata = f"""<?xml version="1.0" encoding="UTF-8"?>
    <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
        <Image ID="Image:0">
            <!-- Minimum required fields about image dimensions -->
            <Pixels DimensionOrder="XYCZT"
                    ID="Pixels:0"
                    SizeC="{bands}"
                    SizeT="1"
                    SizeX="{width}"
                    SizeY="{height}"
                    SizeZ="1"
                    Type="{data_type}"
                    PhysicalSizeX="{CalibrationX}"
                    PhysicalSizeXUnit="{CalibrationUnits}"
                    PhysicalSizeY="{CalibrationY}"
                    PhysicalSizeYUnit="{CalibrationUnits}">
            </Pixels>
        </Image>
    </OME>"""

    out.set_type(pyvips.GValue.gstr_type, "image-description", metadata)
    out.set_progress(True)
    out.signal_connect('eval', eval_cb)
    
    out.write_to_file(outfile, compression='lzw', tile=True, tile_width=512, tile_height=512,  pyramid=True, subifd=True, bigtiff=True)