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Case study

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


Being well-organized

Being well-organized from the start will save you a lot of time. Do you already have a filename convention? If not, here’s a suggestion: include all relevant variables in your filenames, and use a dedicated character to separate them. This will help keep everything structured and easy to navigate.

For example, I use the underscore _ as a separator and arrange variables in a logical, hierarchical order.


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


Renaming files afterward

If you missed the opportunity to name your files using a proper convention, it’s not the end of the world. Tools such as Bulk Rename Utility on Windows or Automator on macOS can quickly and efficiently rename large sets of files.

Run global measurements

A first step is to run a global measurements on all images. This will produce a file with all measurements for all images. We can then use this data to use existing exploratory data visualization tools


  • oogle Data Studio (Looker Studio)
    Free, works in browser, can connect to CSV/Sheets/BigQuery. Very interactive dashboards.

  • Plotly Chart Studio
    Online version of Plotly → drag & drop or upload CSV, make interactive scatterplots, heatmaps, 3D plots.

  • RAWGraphs (https://rawgraphs.io/

  • Napari hub (cloud instances via Binder or Google Colab)
    You can run napari in the browser via Colab or mybinder.org → no local install.

  • JupyterLite / JupyterLab in the browser
    Runs Python + visualization libraries (plotly, bokeh, altair) directly in your browser, no installation.

  • Observable (https://observablehq.com/

Trust your eyes

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





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