Templier (2019)
MagC, magnetic collection of ultrathin sections for volumetric correlative light and electron microscopy
The non-destructive collection of ultrathin sections onto silicon wafers for post-embedding staining and volumetric correlative light and electron microscopy traditionally requires exquisite manual skills and is tedious and unreliable. In MagC introduced here, sample blocks are augmented with a magnetic resin enabling remote actuation and collection of hundreds of sections on wafer. MagC allowed the correlative visualization of neuroanatomical tracers within their ultrastructural volumetric electron microscopy context.
Learn MoreData
templier19_dataset_1 
i 
Example cutout
# pip install numpy tifffile cloud-volume import numpy as np import tifffile from cloudvolume import CloudVolume vol = CloudVolume( "s3://open-neurodata/templier/Wafer1/C1_EM", mip=0, use_https=True ) # load data into numpy array cutout = vol[17920:18432, 22528:23040, 256:272] # save cutout as TIFF tifffile.imwrite("data.tiff", data=np.transpose(cutout))
Documentation for cloud-volume located here
templier19_dataset_2 i
Example cutout
# pip install numpy tifffile cloud-volume import numpy as np import tifffile from cloudvolume import CloudVolume vol = CloudVolume( "s3://open-neurodata/templier/Wafer3/EM", mip=0, use_https=True ) # load data into numpy array cutout = vol[8704:9216, 8704:9216, 0:16] # save cutout as TIFF tifffile.imwrite("data.tiff", data=np.transpose(cutout))
Documentation for cloud-volume located here
Publications
T. Templier and T. Thomas. MagC, magnetic collection of ultrathin sections for volumetric correlative light and electron microscopy. eLife, 2019.
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