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BacTrack User Tutorial

BacTrack feature written and video tutorial: \

Tutorial

To start, either:

Setup new experiment

You must prepare, beforehand, three folders: red, green and blue (each containing image sequence of the appropriate channel).
Images must be 8-bit PNGs, and must be named unanimously (having the same name, and increasing number at the end), e.g.:

  • prpdesGFPmCherryWag05prop01_32_white0000.png
  • prpdesGFPmCherryWag05prop01_32_white0001.png
  • prpdesGFPmCherryWag05prop01_32_white0002.png

Don't worry, ImageJ will do this for you (by deafault), if you say File→Save As→Image sequence. Also, note that once you've processed the movie (i.e. performed cell segmentations) you can measure on a whole different set of images (typically original TIFFs), as long as the ROIs (cell selections) hit the same spot. These folders should not be moved afterwards (in this version) - the program will expect images to be at the same place when you (later) load the experiment. Should you move them, you'll have to edit the experiment properties and set the new file locations. In other words, images WILL NOT be saved to database, only the calculated/defined ROIs, measurements etc.

Load experiment

Use Alt+2 or Experiment→Load experiment. Pick an existing experiment and wait for the experiment to load. If you don't see the images on the R/G/B channels, that probably means that you haven't set up the folders right (see above), or you received a database from someone else and need to point the R/G/B folders to new locations. Either way:

Edit experiment (settings)

Once you've loaded the experiment you can change it's settings via Experiment→Edit current experiment or Alt+4.
You'll get a dialog like this one:

The most common use case for changing the experiment settings is when someone sends you his or hers database and adjoining image files.
Since they've probably stored the in the different folder (than you), you'll have to change this folder paths in order for the images to load.

Delete experiment

To delete the experiment chose Alt+3 or Experiment→delete.
This will not delete the image files on your disk, just the records in the database pertaining to that experiment.

Video Tutorial

Video explaining BacTrack structure and where to store experiment images and databases.

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