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

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:

• On Windows: Bulk Rename Utility
• On Mac: Automator

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

• SAPHIR from Germani E et al.
• Image Data Explorer from Muller C et al.
• ExPanD from Joachim Gassen
• Exploratory from Jin Kim

• 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.