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tut [2013/12/13 15:36]
igor
tut [2014/06/05 13:53] (current)
igor
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-====== BacTrack User Tutorial ====== 
  
-BacTrack feature written and video tutorial: +===== Video Tutorial =====
-\\\+
  
 +==== 1. BactImAs structure and Phase 1  ====
 +Video explaining BactImAs structure and where to store experiment images and databases.
 +{{youtube>​B_A87dSbhP8?​large|BacTrack structure}}
  
-===== Tutorial ===== 
  
-To start, either: ​                                                                                                                                              +==== 2. New experiment ​ ==== 
-  +Video explaining how to define new experiment, and set the initial cell ROIs.
-==== Setup new experiment ==== +
-                                                                                                                                        +
  
-You must prepare, beforehand, three folders: red, green and blue (each containing image sequence of the appropriate channel). \\                              +{{youtube>​fEv40wU9x_Y?large|New experiment}}
-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: +
- +
-{{:​editexperiment.png?200|}} +
- +
-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. +
- +
-==== Edit experiment (settings) ==== +
-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 =====+
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