Booritas

Driver ID	File format	File extensions
SVS	Aperio SVS	*.svs
AFI	Aperio AFI - Fluorescent images	*.afi
SCN	Leica SCN images	*.scn
CZI	[Zeiss CZI](https://www.zeiss.com/microsc

Booritas

# Load input scene from a scn file
scene = slideio.open_slide(input_path, 'AUTO').get_scene(0)
params = slideio.SVSJpegParameters()
params.quality = 75 # compression quality
output_path = "./temp/converted.svs"
delete_file(output_path)
# Saving scene as SVS file
scene.save_image(params,output_path)

Booritas

params = slideio.ColorTransformation()
params.color_space = slideio.ColorSpace.GRAY
transformed_scene = scene.apply_transformation([params])
image = transformed_scene.read_block(size=(0,500))

Booritas

slide = slideio.open_slide(path,'DCM')
scene = slide.get_scene(0)
raw_metadata = scene.get_raw_metadata()
metadata = json.loads(raw_metadata)
modality = metadata['00080060']['Value'][0]

Booritas

slide = slideio.open_slide(image_path,"SVS")
raw_string = slide.raw_metadata

Booritas

rect = (50, 50, 10000, 10000) # read block with ofsets (50,50) from the left top corner and size (10000x10000) pixels
size = (500, 0) # resize block to 500x500 size (the height will be computed automaticaly to avoid image distorsion
block = scene.read_block(rect, size=size, channel_indices=[2]) # read the block to numpy array

Booritas

num_scenes = slide.num_scenes
scene = slide.get_scene(0)
block = scene.read_block()

Booritas

import slideio
slide = slideio.open_slide(image_path,'SVS')

Booritas

import slideio
slide = slideio.open_slidei(file_path="/data/a.czi",driver_id="CZI")
scene = slide.get_scene(0)
block = scene.read_block()

Booritas

python -m pip install slideio