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usage:batch_processing [2019/12/20 18:13] – [Editing the Double FAST script] pseudomoaner | usage:batch_processing [2020/06/26 11:48] (current) – [Installing Double FAST] pseudomoaner | ||
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The .m files required to run Double FAST are included in the main distribution of FAST, available from the [[setup: | The .m files required to run Double FAST are included in the main distribution of FAST, available from the [[setup: | ||
- | Double | + | To run, double |
- | ===== Editing the Double FAST script ===== | + | ===== Using Double FAST script ===== |
To run Double FAST, you will need to perform two tasks: | To run Double FAST, you will need to perform two tasks: | ||
- Run FAST once on a single dataset, using the standard GUI. This generates files containing the settings used for each stage of the analysis. | - Run FAST once on a single dataset, using the standard GUI. This generates files containing the settings used for each stage of the analysis. | ||
- | - Directly edit the DoubleFAST.m script. | + | - Set up the DoubleFAST.m script. |
- | If you are not used to editing code directly, don't panic! All you need to do is tell the software where your datasets are, and what stages in the analysis you would like to perform. By leaving these stages in your hands, | + | If you are not used to editing code directly, don't panic! All you need to do is tell the software where your datasets are, and what stages in the analysis you would like to perform. By leaving these stages in your hands, |
Once you have run FAST on your initial dataset, open the DoubleFAST.m script, available within the DoubleFast directory of your FAST installation. At the top of this script are the key variables that you need to define. | Once you have run FAST on your initial dataset, open the DoubleFAST.m script, available within the DoubleFast directory of your FAST installation. At the top of this script are the key variables that you need to define. | ||
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By default, this is set up assuming a root-branch structure as shown below: | By default, this is set up assuming a root-branch structure as shown below: | ||
- | < | + | {{ :usage:batchprocessfiles.png? |
- | | RRR | | | | | | | | | |RRR{background-color:# | + | |
- | | |!| | | | | | | | | | | + | |
- | | |)|-|-| EE1 | | | | |EE1{background-color:# | + | |
- | | |!| | | |!| | | | | | | + | |
- | | |!| | | |`|-|-| IM1 |IM1{background-color:# | + | |
- | | |!| | | | | | | | | | | + | |
- | | |)|-|-| EE2 | | | | | |EE2{background-color:# | + | |
- | | |!| | | | | | | | | | | + | |
- | | |`|-|-| EE3 | | | | | |EE3{background-color:# | + | |
- | </ | + | |
However, this can be flexibly adjusted according to your requirements. The only requirement is that **batchRoots** is defined as a cell array containing the paths to all of your datasets. | However, this can be flexibly adjusted according to your requirements. The only requirement is that **batchRoots** is defined as a cell array containing the paths to all of your datasets. | ||
- | In the second part of the script, you tell Double | + | Next, if your datasets are not pre-formatted (i.e. have not been set up according to the format specified by the [[usage: |
<code matlab> | <code matlab> | ||
%Filename of the unprocessed image data (Only need to define this if you are running from raw images) | %Filename of the unprocessed image data (Only need to define this if you are running from raw images) | ||
- | imgName = 'Dataset 1.czi'; | + | imgName = 'Img.czi'; |
+ | </ | ||
+ | Note that all of your raw files should have the same name, with their identity specified by their position in the file structure. For example, to process replicate 1 of experimental condition 2, you would give the corresponding raw dataset the filename ' | ||
+ | |||
+ | Finally, you tell Double FAST where it can find the settings files defined during the initial run through FAST: | ||
+ | |||
+ | <code matlab> | ||
%The location of the metadata file output during image import (if the bioformats import system is used) | %The location of the metadata file output during image import (if the bioformats import system is used) | ||
MetadataLoc = ' | MetadataLoc = ' | ||
Line 65: | Line 61: | ||
%The location of the track data generated following the object tracking stages | %The location of the track data generated following the object tracking stages | ||
TrackSettingsLoc = ' | TrackSettingsLoc = ' | ||
+ | |||
+ | %The location of the track data with divisions detected | ||
+ | DivisionSettingsLoc = ' | ||
</ | </ | ||
- | ===== Video demonstration ===== | + | If you wish to leave out some part of the [[usage: |
+ | |||
+ | <code matlab> | ||
+ | %The location of the metadata file output during image import (if the bioformats import system is used) | ||
+ | MetadataLoc | ||
+ | |||
+ | %The location of the segmentParams file saved following image segmentation | ||
+ | SegmentSettingsLoc | ||
+ | |||
+ | %The location of the featSettings file output following feature extraction | ||
+ | FeatureSettingsLoc | ||
+ | |||
+ | %The location of the track data generated following the object tracking stages | ||
+ | %TrackSettingsLoc | ||
+ | |||
+ | %The location of the track data with divisions detected | ||
+ | %DivisionSettingsLoc | ||
+ | </ | ||
+ | |||
+ | Once you have finished setting up Double FAST, you can run it simply by pressing the ' |