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man [2013/12/20 11:12]
igor [4.2. Cell measurements]
man [2014/06/03 10:08] (current)
igor
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-====== ​BacTrack ​User Manual ======+====== ​BactImAs ​User Manual ======
  
-===== 1. BacTrack ​GUI =====                                                                                                                                           +===== 1. BactImAs ​GUI =====                                                                                                                                           
-Image below shows the BacTrack ​GUI. +Image below shows the BactImAs ​GUI. 
  
 GUI consists of three main parts: ​ GUI consists of three main parts: ​
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 ===== 2. Experiment =====                                                                                                                                          ​ ===== 2. Experiment =====                                                                                                                                          ​
    
 +//**Note: please read the installation instructions first, especially the "​BactImAs structure"​ part.**//
 +
 +
 ==== 2.1. Setup new experiment ==== ==== 2.1. Setup new experiment ====
                                                                                                                                         ​                                                                                                                                         ​
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 Should you move them, you'll have to edit the experiment properties and set the new file locations. 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.                                                  ​ In other words, images WILL NOT be saved to database, only the calculated/​defined ROIs, measurements etc.                                                  ​
 +
 +Once the folders are prepared (note that these can be stored anywhere (local hardrive, external server... but it is highly recommended to keep them in the default location under data/images folder). Start BactImAs.jar and select Experiment->​New experiment.  ​
 +You will be asked to choose folders for each channel (“Red”, “Green” and “Blue”. ​ (the location you define in this step will be saved but can be changed later  if you decide to move the folders). Then you must give an unique name to your experiment. Next to this name, BactImAs ​ automatically assigns exp. id (e.g. id 1076) that can be later used in SQL queries. BactImAs will then load images in a few sec and you are ready to start the time-lapse movie processing. ​
 +
 +Optional: This is a good time to also define here some important experimental settings such as pixel size. However, you can also do it at any other time. 
                                                                                                                                                                                                                                                                                                                                
 ==== 2.2. Load experiment ==== ==== 2.2. Load experiment ====
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 Before describing the tracking via built-in algorithm, a quick note on the BactTrack modular structure. \\ Before describing the tracking via built-in algorithm, a quick note on the BactTrack modular structure. \\
-BacTrack ​is designed to be a "​platform for the cell segmentation and tracking"​ and should, ideally, be able to handle any such task. +BactImAs ​is designed to be a "​platform for the cell segmentation and tracking"​ and should, ideally, be able to handle any such task. 
-We recognize that there is no single algorithm suitable for all kinds of tracking tasks and have therefore enabled for various algorithms to be included in the BacTrack ​Platform and used for cell segmentation.+We recognize that there is no single algorithm suitable for all kinds of tracking tasks and have therefore enabled for various algorithms to be included in the BactImAs ​Platform and used for cell segmentation.
 While algorithm design is more a task for the developers (please, see Devs documentation),​ the user, on the other hand, has the option to use any of the available algorithms. ​ While algorithm design is more a task for the developers (please, see Devs documentation),​ the user, on the other hand, has the option to use any of the available algorithms. ​
 Not only can different algorithms be used for different experiments,​ the user can assign different algorithms for different frames of the same experiment! \\ Not only can different algorithms be used for different experiments,​ the user can assign different algorithms for different frames of the same experiment! \\
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 Once cells are segmented, various measurements are acquired in a fully automated way.\\ Once cells are segmented, various measurements are acquired in a fully automated way.\\
-BacTrack ​separates these two processes which has a nice side-effect that, for instance, cell segmentation and tracking can be outsourced or performed by a different person than a person taking measurements. +BactImAs ​separates these two processes which has a nice side-effect that, for instance, cell segmentation and tracking can be outsourced or performed by a different person than a person taking measurements. 
-Using BacTrack's (color) reports (described above), it is easy to visually inspect the quality of the segmentation process.\\+Using BactImAs's (color) reports (described above), it is easy to visually inspect the quality of the segmentation process.\\
  
  
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 Cells are measured using the "​Measure"​ command. User can chose to take any or all available ImageJ measures on the assigned channel (r,g,b). Cells are measured using the "​Measure"​ command. User can chose to take any or all available ImageJ measures on the assigned channel (r,g,b).
 If you want to measure the same attribute on the different channels (e.g. mean on red and green channel) you have to measure twice: first on green and then on red channel (or vice versa). If you want to measure the same attribute on the different channels (e.g. mean on red and green channel) you have to measure twice: first on green and then on red channel (or vice versa).
-When saving measurements in the database ​BacTrack ​behaves in the following way:\\+When saving measurements in the database ​BactImAs ​behaves in the following way:\\
 (a) if the same measurement on the same channel already exists - it is overwritten \\ (a) if the same measurement on the same channel already exists - it is overwritten \\
 (b) otherwise, measurement is saved (added to the already existing measurements) \\ (b) otherwise, measurement is saved (added to the already existing measurements) \\
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 You can repeat the measuring process arbitrary number of times, or measure (repeat for) just a assigned number of frames, etc. You can repeat the measuring process arbitrary number of times, or measure (repeat for) just a assigned number of frames, etc.
  
-BacTrack ​provides a number of additional, derived measures, defined as follows:+BactImAs ​provides a number of additional, derived measures, defined as follows:
 (note that you must first measure area, mean on all channels and background fluorescences on all channels for these measures to be available): (note that you must first measure area, mean on all channels and background fluorescences on all channels for these measures to be available):
  
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 ==== 6.1. Lineage tree visualization ==== ==== 6.1. Lineage tree visualization ====
  
-BacTrack ​features the innovative lineage tree visualization that can map two, user selected, parameters to the cell division tree.+BactImAs ​features the innovative lineage tree visualization that can map two, user selected, parameters to the cell division tree.
 When you're done with measurements,​ choose Reports->​BTree from the main menu. \\ When you're done with measurements,​ choose Reports->​BTree from the main menu. \\
 The following dialog appears:\\ The following dialog appears:\\
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   * convert to hours - whether to convert time in seconds to format: HH:MM:SS   * convert to hours - whether to convert time in seconds to format: HH:MM:SS
  
-BacTrack ​will draw a separate visualization for every cell present on the firt (non-igored) frame.+BactImAs ​will draw a separate visualization for every cell present on the firt (non-igored) frame.
 The following image shows a sample visualization from the demo database: The following image shows a sample visualization from the demo database:
  
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-It is our intention to include in the new version of BacTrack ​additional out-of-the-box statistics and visualization.+It is our intention to include in the new version of BactImAs ​additional out-of-the-box statistics and visualization.
 However, acknowledging that it will never be possible to cover all potential requirements,​ we've enabled the following option: However, acknowledging that it will never be possible to cover all potential requirements,​ we've enabled the following option:
  
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 ==== 6.3. SQL Pane ==== ==== 6.3. SQL Pane ====
  
-BacTrack ​stores all the data (except images) in the SqLite database. \\+BactImAs ​stores all the data (except images) in the SqLite database. \\
 Database can be accessed using any of the SqLite client tools - there are many such tools freely available on the Internet. Database can be accessed using any of the SqLite client tools - there are many such tools freely available on the Internet.
 It is also possible to access it using the simple built-in SQL Pane editor, which allows for arbitrary SQL statements (queries) to be executed and displayed in a table, and even exported as CSV. \\ It is also possible to access it using the simple built-in SQL Pane editor, which allows for arbitrary SQL statements (queries) to be executed and displayed in a table, and even exported as CSV. \\
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 Of course, to use SQL pane one has to know the SQL programming language. Of course, to use SQL pane one has to know the SQL programming language.
-It is our intention, for the future releases of BacTrack, to build a library of predefined SQL queries, with adjoining descriptions in natural language, so that +It is our intention, for the future releases of BactImAs, to build a library of predefined SQL queries, with adjoining descriptions in natural language, so that 
 a user that has no knowledge of SQL language can pick from the set the available predefined queries and retrieve results for his or hers experiment. a user that has no knowledge of SQL language can pick from the set the available predefined queries and retrieve results for his or hers experiment.
  
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 ==== 7.2. Upgrade ==== ==== 7.2. Upgrade ====
  
-When upgrading ​BacTrack, it is best to: \\ +When upgrading ​BactImAs, it is best to: \\ 
-(a) extract new BacTrack ​version into a new folder \\+(a) extract new BactImAs ​version into a new folder \\
 (b) copy the old version'​s data folder over(write) the new version'​s data folder. \\ (b) copy the old version'​s data folder over(write) the new version'​s data folder. \\
  
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 ==== 7.3. Data exchange ==== ==== 7.3. Data exchange ====
  
-(see also the BacTrack ​structure in the User->​Installation)+(see also the BactImAs ​structure in the User->​Installation)
 To exchange data, it is necessary to exchange database and images folder (best zipped). To exchange data, it is necessary to exchange database and images folder (best zipped).
  
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   * Person A sends the images folder (best zipped) to person B. Person B saves (extracts) them to person B's images folder. One could use cloud storage for this steps (eg Dropbox, GDrive) as images are too big for email.   * Person A sends the images folder (best zipped) to person B. Person B saves (extracts) them to person B's images folder. One could use cloud storage for this steps (eg Dropbox, GDrive) as images are too big for email.
-  * Person A sends the bactrack.s3db file (database) from dbs folder to person B. Person B potentially renames it (to avoid clashing with person B's database), saves it to the dbs folder, and adjust the URL in the conf/​db.properties to point to this new database (see User->​Installation)  ​+  * Person A sends the BactImAs.s3db file (database) from dbs folder to person B. Person B potentially renames it (to avoid clashing with person B's database), saves it to the dbs folder, and adjust the URL in the conf/​db.properties to point to this new database (see User->​Installation)  ​
  
 The second step can be repeated if there are new data measured in the database, while the first step needs to be done only once. The second step can be repeated if there are new data measured in the database, while the first step needs to be done only once.
  
  
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