Landscape Three-dimensional single-cell transcriptome imaging of thick tissues¶

Data obtained from https://elifesciences.org/reviewed-preprints/90029v1

In [1]:

import celldega as dega
import pandas as pd

import celldega as dega import pandas as pd

/Users/feni/Documents/celldega/dega/lib/python3.12/site-packages/h5py/__init__.py:36: UserWarning: h5py is running against HDF5 1.14.5 when it was built against 1.14.6, this may cause problems
  _warn(("h5py is running against HDF5 {0} when it was built against {1}, "

In [2]:

base_url = 'https://raw.githubusercontent.com/broadinstitute/scverse-owkin_thick_merfish/main/landscape_files'

base_url = 'https://raw.githubusercontent.com/broadinstitute/scverse-owkin_thick_merfish/main/landscape_files'

In [3]:

landscape = dega.viz.Landscape(
    technology='Xenium', 
    height=600,
    base_url = base_url,
    rotation_x=90
)

landscape = dega.viz.Landscape( technology='Xenium', height=600, base_url = base_url, rotation_x=90 )

/var/folders/8d/jxpy9rd10j7fp2rcj_s5sz3c0000gq/T/ipykernel_64996/3681973614.py:1: UserWarning: Transformation matrix not found at https://raw.githubusercontent.com/broadinstitute/scverse-owkin_thick_merfish/main/landscape_files/micron_to_image_transform.csv. Using identity.
  landscape = dega.viz.Landscape(

In [4]:

df_sig = pd.read_parquet(base_url + '/df_sig.parquet')
mat = dega.clust.Matrix(df_sig)
mat.norm(axis='row', by='zscore')
mat.cluster()
cgm = dega.viz.Clustergram(matrix=mat, width=500, height=500)

df_sig = pd.read_parquet(base_url + '/df_sig.parquet') mat = dega.clust.Matrix(df_sig) mat.norm(axis='row', by='zscore') mat.cluster() cgm = dega.viz.Clustergram(matrix=mat, width=500, height=500)

In [5]:

dega.viz.landscape_clustergram(landscape, cgm)

dega.viz.landscape_clustergram(landscape, cgm)

Out[5]:

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