our code:
from valis import registration
import os
slide_src_dir = "/data_sda/lxt/MSI/MSI-Register"
slides = os.listdir(slide_src_dir)
IHC_slide = [slide for slide in slides if 'HE' not in slide][0]
HE_slide = [slide for slide in slides if 'HE' in slide][0]
IHC_slide_name = IHC_slide.replace('.svs','')
results_dst_dir = "/data_sda/lxt/MSI/Register_results"
registered_slide_dst_dir = os.path.join(results_dst_dir,IHC_slide_name)
os.makedirs(registered_slide_dst_dir,exist_ok=True)
reference_slide = os.path.join(slide_src_dir,HE_slide)
registrar = registration.Valis(slide_src_dir, results_dst_dir,reference_img_f=reference_slide)
rigid_registrar, non_rigid_registrar, error_df = registrar.register()
registrar.register_micro(max_non_rigid_registration_dim_px=2000, align_to_reference=True)
registrar.warp_and_save_slides(registered_slide_dst_dir, crop="reference",compression='jpeg',Q=5)
registration.kill_jvm()

our code:
from valis import registration
import os
slide_src_dir = "/data_sda/lxt/MSI/MSI-Register"
slides = os.listdir(slide_src_dir)
IHC_slide = [slide for slide in slides if 'HE' not in slide][0]
HE_slide = [slide for slide in slides if 'HE' in slide][0]
IHC_slide_name = IHC_slide.replace('.svs','')
results_dst_dir = "/data_sda/lxt/MSI/Register_results"
registered_slide_dst_dir = os.path.join(results_dst_dir,IHC_slide_name)
os.makedirs(registered_slide_dst_dir,exist_ok=True)
reference_slide = os.path.join(slide_src_dir,HE_slide)
registrar = registration.Valis(slide_src_dir, results_dst_dir,reference_img_f=reference_slide)
rigid_registrar, non_rigid_registrar, error_df = registrar.register()
registrar.register_micro(max_non_rigid_registration_dim_px=2000, align_to_reference=True)
registrar.warp_and_save_slides(registered_slide_dst_dir, crop="reference",compression='jpeg',Q=5)
registration.kill_jvm()