> For the complete documentation index, see [llms.txt](https://stitchit.mouse.vision/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://stitchit.mouse.vision/new-users/the-experiment-directory-structure.md).

# Directory structure

*StitchIt* expects certain data to be located in certain locations within the experiment root directory. These locations are defined in the [INI file](/installation/setting-up-the-ini-file.md). You shouldn't change these values unless you know what you're doing. `syncAndCrunch` honors the locations defined in the INI when it copies data from the acquisition server to the local device. The default data directories are:

```
EXP_ROOT_DIR/
   Mosaic_Sample_I.txt
   rawData/
     Sample_I-0001/
      acquisition_log.txt
        COMPLETED
        sectionPreview.mat
        SL_1122247-0001_00001.tif
        SL_1122247-0001_00002.tif
        SL_1122247-0001_00003.tif
        [etc]
        tileIndex
        tilePositions.mat
     stitchitPreProcessingFiles
           tileStats_ch2.mat  
           tileStats_ch3.mat
           tileStats_ch4.mat
           averages/
             1/
             2/

   stitchedImages_100/
     1/
      section_001_01.tif
      section_001_02.tif
      [etc]
     2/
      section_001_01.tif
      section_001_02.tif
      [etc]
```

The `stitchedImages_100` directory is created following stitching. The `averages` directory is created during processing. The main thing to get right is ensure there is a `rawData` directory and in this are the directories produced by the acquisition software. `syncAndCrunch` will do this.