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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
List all your files 
On Windows using a Cmd 
cd Your\Path\Here
dir /b /a-d > YourFileList.txt

On MacOS
cd "Your/Path/Here"
ls -1 > 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 during acquisition, it’s not the end of the world. There are tools that 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


  • Google 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.