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Case study

You are back from your acquisition session at the microscope with some images taken all the same way. What about now?

Being well-organized

Being well organized from the beignin will save you a lot of time. Do you have a filename nomenclature? If not, here is my suggestion: Include all relevant variables in your filename. Use a dedicated character to separate them. Keep them organized and well ordered.

For example I use an underscore _ as a separator. I order variables in a hierachic manner.

VariableA-001_VariableB-01_VariableC-0.tif

In the example below I have 3 variables:

  • Slides with 5 levels: 1-5
  • Coverslips with 3 levels: 1-3
  • Images with 3 levels: 1-3
MyListofFiles 
In Windows Cmd 

cd Your\Path\Here
dir /b /a-d > YourFileList.txt

Slide-001_Coverslip-01_Image-01.czi
Slide-001_Coverslip-01_Image-02.czi
Slide-001_Coverslip-01_Image-03.czi
Slide-001_Coverslip-02_Image-01.czi
Slide-001_Coverslip-02_Image-02.czi
Slide-001_Coverslip-02_Image-03.czi
Slide-001_Coverslip-03_Image-01.czi
Slide-001_Coverslip-03_Image-02.czi
Slide-001_Coverslip-03_Image-03.czi
Slide-002_Coverslip-01_Image-01.czi
Slide-002_Coverslip-01_Image-02.czi
Slide-002_Coverslip-01_Image-03.czi
Slide-002_Coverslip-02_Image-01.czi
Slide-002_Coverslip-02_Image-02.czi
Slide-002_Coverslip-02_Image-03.czi
Slide-002_Coverslip-03_Image-01.czi
Slide-002_Coverslip-03_Image-02.czi
Slide-002_Coverslip-03_Image-03.czi
Slide-003_Coverslip-01_Image-01.czi
Slide-003_Coverslip-01_Image-02.czi
Slide-003_Coverslip-01_Image-03.czi
Slide-003_Coverslip-02_Image-01.czi
Slide-003_Coverslip-02_Image-02.czi
Slide-003_Coverslip-02_Image-03.czi
Slide-003_Coverslip-03_Image-01.czi
Slide-003_Coverslip-03_Image-02.czi
Slide-003_Coverslip-03_Image-03.czi
Slide-004_Coverslip-01_Image-01.czi
Slide-004_Coverslip-01_Image-02.czi
Slide-004_Coverslip-01_Image-03.czi
Slide-004_Coverslip-02_Image-01.czi
Slide-004_Coverslip-02_Image-02.czi
Slide-004_Coverslip-02_Image-03.czi
Slide-004_Coverslip-03_Image-01.czi
Slide-004_Coverslip-03_Image-02.czi
Slide-004_Coverslip-03_Image-03.czi
Slide-005_Coverslip-01_Image-01.czi
Slide-005_Coverslip-01_Image-02.czi
Slide-005_Coverslip-01_Image-03.czi
Slide-005_Coverslip-02_Image-01.czi
Slide-005_Coverslip-02_Image-02.czi
Slide-005_Coverslip-02_Image-03.czi
Slide-005_Coverslip-03_Image-01.czi
Slide-005_Coverslip-03_Image-02.czi
Slide-005_Coverslip-03_Image-03.czi

If you missed the opportunity to name your file with a proper nomenclature this is not the end of the world. BulkRenameUtility for windows  is equivalent to Automator on MacOS and can rename files in a breeze.

Run global measurements


Trust your eyes

First thing you should do: Open few images and look at them.





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