Skip to content

Latest commit

 

History

History
63 lines (40 loc) · 2.54 KB

faq.md

File metadata and controls

63 lines (40 loc) · 2.54 KB
Raw

TissueMiner FAQ

How do I run snakemake with a project specific configuration file instead of default_config.R?

  • For running TissueMiner API Export a shell variable named TM_CONFIG pointing to the config file you would like to use. E.g. to use config/flywing_tm_config.R, before running snakemake, just do
export TM_CONFIG=$TM_HOME/config/flywing_tm_config.R
  • For running TissueMiner snakemake workflow
    • Ubuntu: export TM_CONFIG=$TM_HOME/config/flywing_tm_config.R
    • Docker: defined my_config.R in the movie repository and run the command below
    alias tm='docker run --rm -ti -v $(dirname $PWD):/movies -w /movies/$(basename $PWD) -u rstudio etournay/tissue_miner'
tm "export TM_CONFIG=/movies/my_config.R; sm all"

What kind of data are required to run TissueMiner ?

TissueMiner uses the cell tracking information from TissueAnalyzer, which implies that cell tracking must have been done in TissueAnalyzer. Two masks - tracked_cell_resized.tif and cell_division.tif - from TissueAnalyzer are read by TissueMiner. These 2 masks are required.

In addition, the user must provide the cumulative time (in seconds) of the movie, in a file called cumultimesec.txt

Can the cell segmentation procedure be done with another tool ?

Yes, it can. Any segmentation tool that would produce a binary segmentation mask can be used in TissueAnalyzer for further cell tracking. Only the tracking step in TissueAnalyzer is currently required for TissueMiner to work.

Is TissueAnalyzer part of TissueMiner ?

TissueMiner works downstream of TissueAnalyzer. Therefore TissueAnalyzer is included in the TissueMiner framework.

How to change the number of digits used for padding ?

Edit the tm.snkmk file located in the workflow folder, and find and replace %03d by the desired padding (ex: %04d for 4 digits).

How to update my TissueMiner installation?

On the docker plateform (Linux, MacOs, Windows) simply pull latest image again with

docker pull etournay/tissue_miner

On ubuntu simply fetch the changes by

cd  ${TM_HOME} && git pull origin && cd parser && make clean all

How to force git pull origin in case of conflict ?

Caution: if you do this, you may lose all of your local changes in tissue_miner

git fetch --all
git reset --hard origin/master