Extracting cells from with specific criteria

asundaresan · July 10, 2025, 11:05pm

Hello,

I am trying to extract the cells along with the gene expression , which belong to the PSTN anatomical structure (part of HY anatomical division) with the criteria of Crh gene expression in a specific range.

I have tried to use the instructions from this notebook but I am not able to select the specific cells with the above mentioned criteria.

Can you let me know how I can go about extracting this?

Thanks

Dataset - MERFISH-C57BL6J-638850 Reconstructed Coordinates,
CCF mapped coordinates for cells in the whole brain spatial transcriptomics dataset (MERFISH-C57BL6J-638850-CCF)

rachel.hostetler · July 16, 2025, 4:43pm

Hi! Thank you for your question. We are working on a solution for this and will get back to you by the end of the week.

asundaresan · July 23, 2025, 4:29pm

Hi Rachel,

Is there any update on the solution.

Thanks

rachel.hostetler · July 26, 2025, 1:16am

@asundaresan

Thank you for your patience. Here is a link to a Google Colab notebook that should be able to answer your question (getting gene expression data for an anatomical substructure). The notebook is written using the MERFISH-C57BL6J-638850-imputed data, but can be run with MERFISH-C57BL6J-638850 data (not imputed). The notebook also features another filter (restricting cells to a neurotransmitter type), but those lines can be skipped.

Feel free to email me at rachel.hostetler@alleninstitute.org if you have any issues with the notebook or further questions.

github.com/rachelhostetler/ABCAtlas_UseCases

Plotting_MERFISH_imputed_gene_expression_in_NT_and_region_subset.ipynb

main

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/rachelhostetler/ABCAtlas_UseCases/blob/main/Plotting_MERFISH_imputed_gene_expression_in_NT_and_region_subset.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZBQuoGjQqVzc"
      },
      "source": [
        "# Allen Brain Cell Atlas Use Case\n",
        "This notebook is an example of how to use data from the Allen Brain Cell (ABC) Atas. Code for this notebook comes from [ABC Atlas Access](https://alleninstitute.github.io/abc_atlas_access/intro.html), which features in depth tutorials on ABC Atlas scRNAseq and MERFISH datasets. Use ABC Atlas Access to learn more about each of the datasets. The text following '#' are comments and/or indicate where the code can be edited to look at different brain regions, cell types, etc. This notebook is intended to be used in Google Colab.\n",

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Extracting cells from with specific criteria

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