Using scyjava to convert resolutions pyramid VSI file to tif file resaults with 1/40 resolution layer of the pyramid only.

[OriKovacsiKatz]

Hello
My name is Ori , I am an HPC and AI advisor at the Technion (Research Institute and University)
I advise a researcher and need help with medical imaging Olympus resolution issue:
(continuing my email with Edward Evans suggesting me opening my inquiry to the public eye)
Using imageJ with scyjava to convert VSI (Olympus) images to tif format , provide only a small portion
of the imaging binary data.
Specifically there is some imaging images pyramid where the x40 resolution required so the resulting
image is only X 1/40 of the necessary binary details.

How can I force bio-format convert to export tif image with the x40 zoom size out of the VSI Olympus pyramid?

I use the code:
import imagej
from os import listdir
import numpy as np
import os.path
ij = imagej.init(headless=False)

SOURCE_DIRECTORY=r"/home//Data/Melanoma_WSI/H&E/20241027/"
TARGET_DIRECTORY=r"/home//Data/Melanoma_WSI/H&E/20241027_converted/"
def convertImageToTif(image_name):
image_url=SOURCE_DIRECTORY+ image_name
print("# read image:")
print(image_url)
save_url=TARGET_DIRECTORY+image_name.split('.vsi')[0]+'.tif'
print("# write image:")
print(image_url)
jimage = ij.io().open(image_url)
print("# after opening image...")
ij.io().save(jimage, save_url)
print("# after saving image....")

files = np.array(listdir(SOURCE_DIRECTORY))

files in source which contain ".vsi"

files = files[np.flatnonzero(np.core.defchararray.find(files,'.vsi')!=-1)]
print("# converting files:")
print(files)

for file in files:
convertImageToTif(file)