I am trying to determine how the EntityID found in the .parquet file for each of the raw merfish_output dirs from the Yao et al. 2023 Study (e.g. Index of /aa/79/aa79b8ba5b3add56/609882/1198980026/merfish_output/cellpose_cyto2_nuclei/) maps to the cell_label in the ‘reconstructed_coordinates.csv’ and/or ccf_coordinates.csv files found here (AWS S3 Explorer). Is this possible? Perhaps there is another file that you can share with me or direct me to that connects these two different cell labels?
Alternatively, is there a way to determine the brain Z-axis of each of the raw merfish samples (e.g. what z axis is the 1198980026 sample and so on… This way I can reconstruct the 3D geometries myself)
I’m not fully sure I understand what you want to accomplish. I never really worked with the parquet files my self, I believe those contain the polygon for the cell segmentation shapes, so in theory they should have labels that map to the cell id’s.
What do you mean by z-axis exactly? The Z location of the section in the CCF? You can extract these from the ccf_coordinates.csv
Thanks for the response. Last I checked, the cell ids in ccf_coordinates.csv do not match the cell ids in raw data (the parquet file).
If these have been lost somewhere, it would be good to at least know what the actual z values are for each of the sections provided in the first link I shared, so that I can manually register them myself using a different method.