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tut [2013/12/17 17:02] igor |
tut [2014/06/05 13:53] (current) igor |
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| - | ====== BacTrack User Tutorial ====== | ||
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| - | BacTrack feature written and video tutorial: | ||
| - | \\\ | ||
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| - | ===== Tutorial ===== | ||
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| - | To start, either: | ||
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| - | ==== Setup new experiment ==== | ||
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| - | 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. | ||
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| - | ==== 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: | ||
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| - | {{:editexperiment.png?400|}} | ||
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| - | 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. | ||
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| ===== Video Tutorial ===== | ===== Video Tutorial ===== | ||
| - | Video explaining BacTrack structure and where to store experiment images and databases. | + | ==== 1. BactImAs structure and Phase 1 ==== |
| + | Video explaining BactImAs structure and where to store experiment images and databases. | ||
| {{youtube>B_A87dSbhP8?large|BacTrack structure}} | {{youtube>B_A87dSbhP8?large|BacTrack structure}} | ||
| + | ==== 2. New experiment ==== | ||
| + | Video explaining how to define new experiment, and set the initial cell ROIs. | ||
| + | {{youtube>fEv40wU9x_Y?large|New experiment}} | ||
