Which .zarr files should be imported to start

[SofiaIbanezMolero]

Hi!

I am trying to use sparrow for the first time. Out of the Xenium analysis I got different .zarr files "cells.zarr", "cell_feature_matrix.zarr", "analysis.zarr", etc. Which of the .zarr files is needed to get started?
I tried using the path to the folder that contains everything but it does not accept it, so I am not sure if that is the correct way.

Best,
Sofia

[lopollar]

Hi,
You should start from the image, that can be found at morphology_focus.ome.tif
The transcripts cna be found at transcripts.csv.gz.

From the standard tutorial, there is one more addition.

you should run following code before reading in the transcripts. THis is necessary to convert the locations of the transcripts in micrometer, to the image:
`
import pandas as pd

import numpy as np

df=pd.DataFrame([[4.70588235294,0,0],[0,4.70588235294,0],[0,0,0]])
np.array([[4.70588235294,0,0],[0,4.70588235294,0],[0,0,0]]).tofile('transformation_matrix.csv',sep=',')
np.savetxt('transformation_matrix.csv',np.array([[4.70588235294,0,0],[0,4.70588235294,0],[0,0,1]]))
df.to_csv('transformation_matrix.txt')
`

The code to read in the transcripts had to be changed to
sdata = sp.io.read_transcripts(sdata, path_count_matrix=path_coordinates, transform_matrix='transformation_matrix.csv', filter_gene_names=['Unassigned','Control'],column_x=4,column_y=5,column_gene=3,header=0)