I am a new Zeiss user following an established workflow in my lab, with our M.2 microscope and Zen 2.3 pro software. I was referred to this forum by tech support to automate the repetitive batch-processing sequence. In short, my protocol is as follows:
- Draw polygons around all tissue regions for tile acquisition
- Specify Z reference points for each tile set
- Image set of tile regions as z-stacks with each scene saved separately
- Load all scenes into batch processing and perform apotome raw convert
- Empty the batch processing list and load all apotome converted images to perform stitching
Code: Select all
# Prompt User to specify output folder
Outputfolder = ???
# Load the newly acquired image
raw_im = ???
# Perform ApoTome raw convert
nb_phase = image.Bounds.SizeH
image_apotome = Zen.Processing.Utilities.ApoTomeSimConvert(raw_im,
ZenApoTomeProcessingMode.Sectioned,
ZenSimCorrectionMode.LocalIntensity,
ZenNormalizeMode.Clip,
ZenApoTomeFilter.Off,
False)
# Save Processed file
image_name = image.Name.Replace('.czi', '_Apotome.czi')
imageName = Path.Combine(Outputfolder, image_name)
image_apotome.Save(imageName)
# get the stitching settings
Stitchset = r'Stitching_Channel_1.czips'
# create a function setting for the Stiching Function
functionsetting1 = Zen.Processing.Transformation.Geometric.Stitching(image_apotome)
# apply the setting
functionsetting1.Load(Stitchset)
# Save Stitched file
image_name = image.Name.Replace('_Apotome.czi', '_Stitched.czi')
imageName = Path.Combine(Outputfolder, image_name)
functionsetting1.Save(imageName)