Skip to content

Latest commit

 

History

History
136 lines (83 loc) · 6.29 KB

tm_qs_user_data.md

File metadata and controls

136 lines (83 loc) · 6.29 KB

First Use of TissueMiner with your own data

1. First, organize your movie images as follows

  • Create a movie_repository folder where you store the data from all your movies
    • Inside this folder, create one movie folder per movie
      • inside each movie folder, create a Segmentation folder to store movie images
        • the movie should be stored as a series of tif or png files, one per timepoint, with the name of each file composed of a sample name + underscore + frame number

The data organization is summarized as follow:

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

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

Here, is an example: movieSegmentation/demo/Segmentation/demo_000.png

alt tag

  • The image type should be 8-bit or RGB.
  • The image format should be png or tiff

2. 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:

  • get a fresh FIJI installation (including JDK8)
  • 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

3. Optionally, define regions of interest (ROI's) and orient the tissue along the x or y axis

To this purpose, we provide two FIJI programs draw_n_get_ROIcoord.ijm and orient_tissue.ijm.

3.1 Define ROI's:

  • launch FIJI
  • go to the fiji_macros folder located in your TissueMiner installation folder
  • drag-and-drop the draw_n_get_ROIcoord.ijm file into FIJI
  • a script editor opens automatically
  • click RUN and define your ROI's

By default, TissueMiner always creates two ROI's:

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

3.2 Orient the tissue

  • launch FIJI
  • go to the fiji_macros folder located in your TissueMiner installation folder
  • drap-and-drop the orient_tissue.ijm file into FIJI
  • a script editor opens automatically
  • click RUN and define the tissue axis to be aligned on x or y.

Both programs 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.

4. Open a Docker QuickStart Terminal

  • You'll find it either in your application menu or application folder (depending on your system):

alt tag

5. Go to the movie directory

  • Browse your data to find the movie folder
  • In your terminal type in cd and press space
  • and drag-and-drop the movie folder into the terminal

Example: cd /home/tissueminer/movie_repository/movie_1

  • Set up the docker command and store it in a shell variable for simplicity

alias tm='docker run --rm -ti -v $(dirname $PWD):/movies -w /movies/$(basename $PWD) -u rstudio etournay/tissue_miner'

A tip ! Just copy this line above in your .bashrc to make this tm command permanent. This file is the standard configuration file of the Terminal.

6. Select the analysis you are interested in

Here, we propose some streamlined quickstart tutorials.

All tutorials can be used to compare between different regions of interest. Here, we give an example with cell area

Here, run an entire analysis of a single movie

tm "sm shear_calculate topo_countt1 polygon_class tri_categorize; analyze_movie.R . output_analysis"

Here, use your own configuration file to optimize the output rendering. Your configuration file my_config.R must be located in the movie repository folder. You'll find more explanation about this file in the TM R User Manual.

tm "export TM_CONFIG=/movies/my_config.R; sm shear_calculate topo_countt1 polygon_class tri_categorize; analyze_movie.R . output_analysis"

7. Look at the results

  • Where to find the results ?

In the current movie folder, a new output_analysis folder has been created, where you'll find plots and videos created by running the tutorials.

  • Where to find the current movie folder?

In this tutorial, the example data have been downloaded into your home directory, which may be represented with a "house" icon when using a file browser. In your file browser, go to your home directory, then click on example_data, click on demo, and finally on output_analysis. Here, are your results !