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How to process a movie with TissueMiner over your own data

First segment and track cells using TissueAnalyzer

Tissue Analyzer (copyright Aigouy 2016) ships with its own licence (see license_TA.txt bundled in the software). Tissue Analyzer should not be modified or reverse engineered. Tissue Analyzer should always be distributed bundled with TissueMiner and not alone.

You can install the latest version of Tissue Analyzer (formerly known as Packing Analyzer) within FIJI (http://fiji.sc/Fiji). To do so:

  • launch FIJI
  • open the "Help" menu
  • click on "Update..."
  • click on "Manage update sites"
  • click on "Add" and enter "http://sites.imagej.net/TA/" in the URL field (and anything you like in the "Name" field)
  • click "Close" and FIJI should offer you to install TA.

Once the installation is complete, restart FIJI, open the "Plugins" menu and click on "Tissue Analyzer"

For a quick start guide, click here

Options: delimit regions of interest (ROI's) and orient the tissue along the x or y axis

Fiji macros can be found in your local TissueMiner installation or here. Just drad-and-drop the file onto Fiji and click 'run':

  • draw_n_get_ROIcoord.ijm
  • orient_tissue.ijm

Both macros automatically save a text file (UserFrameRoi.txt and transformation.txt, respectively). If these files are present, TissueMiner will take them into account for further precessing steps.

NB: by default, Tissue Miner will always create two ROI's:

  • "raw": corresponds to all segmented and tracked cells
  • "whole_tissue": corresponds to cell lineages that remain in the field of view

Data structure

We invite the user to store all movies in a movie repository folder <movie_repository> to facilitate automated movie comparison.

Here is the required structure of a movie:

<movie_repository>/<movie_directory>/Segmentation/<movie_directory_name>_%03d.png

%03d represents a number padded with 3 digits. The number of digits can be modified FAQ.

All movie images are contained in the Segmentation folder, namely the location images used by Tissue Analyzer to segment and track cells. Upon segmentation and tracking, TissueAnalyzer will generate one folder per image, in this Segmentation folder.

TissueMiner will generate additional folders and files in the <movie_directory> folder.

System Preparation

Ubuntu

First, make sure to have TM_HOME shell variable pointing to the root of your TissueMiner installation as TissueMiner requires it to resolve script paths internally (see code chunck below).

Then, tweak the $PATH to include the tools (see code chunck below).

Finally, we highly recommend to add the next code block lines in your .bashrc or .bash_profile so that you don't have to export the environment variables again.

## adjust your path to include the tissue_miner folder
export TM_HOME="~/tissue_miner"
export

## adjust your path to include all tools for execution
export PATH=$TM_HOME/db:$TM_HOME/shear:$TM_HOME/roi:$TM_HOME/misc:$TM_HOME/movies:$TM_HOME/shear_contributions:$TM_HOME/topology:$TM_HOME/triangles:$TM_HOME/lineage:$PATH
export PATH=${TM_HOME}/parser:$PATH

## defines an alias for the snakemake command line
sm() {
    snakemake --snakefile ${TM_HOME}/workflow/tm.snkmk --keep-going "$@"
}
export -f sm

## Then apply changes
source .bashrc

To run TissueMiner

To run TissueMiner entirely over your own data, you'll need to go to the source directory containing your movie directories (use the cd command + drag and drop the folder corresponding to your movie repository folder onto the shell + press enter) and to replace my_favorite_movie with your movie directory of interest.

## Example for "my_favorite_movie"
cd path_to_your_movie_repository
docker run --rm -ti -v $(pwd):/movies -w /movies/my_favorite_movie brandl/tissue_miner sm all

For a more streamlined analysis, please visit the tutorials here

Once your tracked-cell data have been processed by the TissueMiner automated workflow, you can perform a custom multiscale analysis of epithelial morphogenesis using the detailed R-tutorial or the Python-tutorial.

To run the automated workflow we recommend snakemake. We provide a snakemake workflow to ease running TissueMiner on a cluster or locally on a single computer. It integrates all analyses implemented in TissueMiner and can be easily extended to include project specifc elements as well. This is how we usually run TissueMiner:

##  define a custom snakemake launcher to save typing
sm() {
    snakemake --snakefile ${TM_HOME}/workflow/tm.snkmk --keep-going "$@"
}
export -f sm

## TissueMiner assumes the movie data to be present in the current working directoy
cd <movie_directory>

## List all tasks
sm -n

## Process all tasks and write a log file
sm all | tee log.txt

## ... or just run sepecific tasks
sm make_db | tee log.txt

## Export statistics and execution state graph visualization
sm --dag | dot -Tpdf > dag_tbd.pdf
sm -D > sm_execution_state.txt

For snakemake details see the its reference.

Although we do not recommend it, you can also run each of the TissueMiner tools separately. See simple_workflow.sh for an example pipeline.