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. 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:
1
EXP_ROOT_DIR/
2
   Mosaic_Sample_I.txt
3
   rawData/
4
     Sample_I-0001/
5
        09262015-1329-182_01.tif
6
        09262015-1329-224_02.tif
7
        [etc]
8
        Mosaic_Sample_I-0001.txt
9
        tileIndex
10
​
11
     stitchitPreProcessingFiles
12
           tileStats_ch2.mat  
13
           tileStats_ch3.mat
14
           tileStats_ch4.mat
15
           averages/
16
             1/
17
             2/
18
​
19
   stitchedImages_100/
20
     1/
21
      section_001_01.tif
22
      section_001_02.tif
23
      [etc]
24
     2/
25
      section_001_01.tif
26
      section_001_02.tif
27
      [etc]
Copied!
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.

New users: - Previous

How to...?

Next - FAQ

Common errors

Last modified 1yr ago

Copy link