Image-based Profiling Template

This repository was derived from a template repository located at https://github.com/cytomining/profiling-template. The purpose of the repository is to weld together a versioned data processing pipeline with versioned processed output data for a single image-based profiling experiment.

(Derived from this template)

AFTER GENERATING A NEW REPO, CHANGE OR DELETE ALL NONSPECIFIC DETAILS

Setup

To correctly initialize the repository, we need to perform several manual steps.

Step 0: Create a new repository using this repository as a template

By spinning up a new repo using this repo as a template, you will retain all code, configuration files, computational environments, and directory structure that a standard image-based profiling workflow expects and produces.

Step 1: Fork the profiling-recipe repo

We first want to fork the official profiling recipe located at https://github.com/cytomining/profiling-recipe.

• Result: The fork creates a copy of a recipe repository.
• Goals: 1) Remove the connection to official recipe updates to avoid unintended weld versioning reversal; 2) Enable independent updates to fork code that does not impact official recipe.
• Execution: See forking instructions.

Step 2: Create a submodule inside this repository of the forked recipe

Next, we will create a submodule in this repo.

• Result: Adding a submodule initiates the weld.
• Goals: 1) Link the processing code (recipe) with the data (current repo); 2) Require a manual step to update the recipe to enable asynchronous development.
• Execution: See below

# In your terminal, clone the repository you just created (THIS REPO)
USER="INSERT-USERNAME-HERE"
REPO="INSERT-NAME-HERE"
git clone [email protected]:$USER/$REPO.git

# Navigate to this directory
cd $REPO

# Add the recipe submodule
git submodule add https://github.com/$USER/profiling-recipe.git profiling-recipe

Refer to "Adding a submodule" for more details.

Step 3: Commit the submodule

Lastly, we will commit the submodule to github.

• Result: Committing this change finalizes the weld.
• Goals: 1) Track the submodule (recipe) version with the current repository.
• Execution: See below

# Add, commit, and push the submodule contents
git add profiling-recipe
git add .gitmodules
git commit -m 'finalizing the recipe weld'
git push

Step 4: Fill out experiment information

This step ensures that relevant experimental information is captured. Listed below are experimental details that the Broad Institute Imaging Platform uses. Feel free to adapt to your needs.

When done, delete steps 0-3 and fill out the below. Fill out the whole template on the first batch; for subsequent batches only add what is different.

The Broad Institute Imaging Platform also logs this information in a spreadsheet(Broad-internal access only). The corresponding entry/entries in the sheet should link back to this file.

Cell type : _______ (ex: U2OS)
Cell source: ________ (ex: Collab lab) (ex: GPP)
Plate size : _______ (ex: 384)
Plate brand : _______ (ex: Cell carrier Ultra)
Cell densit(y/ies) : _______ (ex: 2K/well) (ex: Columns A-D 1K/well, Columns G-H 500/well)
Type of perturbation : ___________ (ex: Gene overexpression) (ex: CRISPR KO + compounds)
If (at least partially) genetic: 
    Genetic introduction method : __________ (ex : lentiviral transduction)
    Selection method : _________ (ex: None) (ex: Puromycin 1ug/mL 24 hrs)
    Number of genes : __________ (ex: 384)
    Number of perturbations per gene : __________ (ex: N/A) (ex: 4 guides per gene)
If (at least partially) chemical :
    Number of chemicals : __________ (ex: 384)
    Number of dose points per chemical : _________ (ex: 1)
Number of replicates per perturbation : __________ (ex: 5)
Perturbation time point : _____________ (ex: 72 hrs)
Staining protocol : ____________ (ex: CellPainting v3 (LINK)) (ex: LipocytePainting (CITATION)) (ex: 1:500 gt anti tubulin (cat #), 1:1000 A488 anti gt (cat #))
Microscope : ________ (ex: Opera Phenix ) 
Mode : ________ (ex: Confocal) 
Excitation / emission details : ______________ (ex: ex 488 laser, em 550/50; ex 568 laser, em 600/30) (ex: see Index.idx.xml file)
Objective : _____________ (ex: 20X water 1.0NA)
Binning : ____________ (ex: 1x1)
Sites per well : __________ (ex: 9)
Pixel size : ____________ (ex: 0.656um)
Number of Z planes : _______ (ex: 3)
Z plane spacing : ________ (ex: 1um)