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Enrico Tagliavini edited this page Mar 24, 2023 · 27 revisions

Welcome to the scMultipleX Wiki!

Installation

Create new conda environment with python 3.8+:

conda create -n scmpx python=3.8

Activate the conda environment:

conda activate scmpx

Install scMultipleX:

pip install git+https://github.com/fmi-basel/gliberal-scMultipleX.git

Demo Run of scMultipleX

  1. SSH into [email protected]:

ssh [email protected]

Note to Windows users: use power shell, or Putty.

  1. Create an output directory (ex. username/scMultiplex-demo-test)

mkdir /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR

  1. Copy demo config file (demo.ini) to own user folder

cp -t /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR /tungstenfs/scratch/gliberal/Code/Common/Repositories/gliberal-scMultipleX/resources/scMultipleX_testdata/demo.ini

  1. Check that demo.ini it is copied over: ls /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR

You should see the demo.ini file listed in directory

  1. Edit this config file:
  • Remote into favorite virtual machine
  • Navigate to demo.ini and open it in favorite text editor (e.g. Notepad++)
  • Change base_dir_save to MY_SAVE_DIR path, save.
  1. This step needs to be performed only once per machine and user Make symlink in user home bin directory that points to run_scmultiplex executable:
  • cd $HOME
  • mkdir -p bin
  • ln -s -t bin /tungstenfs/scratch/gliberal/Code/Common/Repositories/gliberal-scMultipleX/run_scmultiplex
  • ls -l bin
  1. Run scMultipleX on test dataset

run_scmultiplex --help

run_scmultiplex --cpus 12 --config /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR/demo.ini --tasks 0 1 2 3 4 5 6 7

  1. Check output folder!

Configuring scMultipleX

[00BuildExperiment] General parameters for initializing FAIM-HCS experiment structure

well_pattern = Regex pattern for recognizing well ID

raw_ch_pattern = Regex pattern for recognizing channel ID

mask_ending = Suffix of organoid segmentation image

base_dir_raw = Path to raw data directory (folder contains rounds)

base_dir_save = Path to save directory

spacing = Z,Y,X pixel spacing of region-extracted data in um/pix, comma-separated

overview_spacing = Y,X pixel spacing of well overview images, comma-separated

round_names = Names of multiplexing rounds, comma-separated

[00BuildExperiment.round_R0] Round-specific parameters for initializing FAIM-HCS experiment structure

name = Round name

nuc_ending = Suffix of nuclear segmentation image

mem_ending = Suffix of membrane segmentation image

root_dir = Path to raw data directory for this round

fname_barcode_index = Number of underscores in Yokogawa barcode, integer

organoid_seg_channel = Image channel used for organoid segmentation, in format 'C01', 'C02', etc.

nuclear_seg_channel = Image channel used for nuclear segmentation, in format 'C01', 'C02', etc.

membrane_seg_channel = Image channel used for membrane segmentation, in format 'C01', 'C02', etc.

Running scMultipleX

scMultipleX is installed on tungsten at: scratch/gliberal/Code/Common/Repositories/gliberal-scMultipleX

and can be run on any machine.

To run on CPU cluster, configure the clusterme.sh file From vcl1043, navigate to folder containing clusterme.sh and run:

sbatch clusterme.sh

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