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Analyze multiple folders at once

Analyzing multiple folders at once (Fig. 11) streamlines high-throughput experimentation by applying validated analysis parameters to entire datasets with minimal user intervention. By configuring folder selection and per-folder arena counts, users ensure that Cellects applies the same detection logic uniformly while respecting experimental heterogeneity.

Detailed description

Select folders to analyze window
Figure 11: Select folders to analyze window

The window of Figure 11 appears after the first window when the selected folder contains subfolders with images matching the Image prefix and Images extension patterns.

Check to select all folders:

Select this option to run the analysis on all folders containing images matching the Image prefix and Images extension. Otherwise, use Ctrl/Cmd to select specific folders for analysis.

Note

  • This setting affects only the Run All functionality.
  • To apply saved masks (e.g., background or specimen initiation regions) across selected folders,enable Keep Cell and Back drawing for all folders in Advanced parameters.

Here, the user can adjust the number of arenas for each folder

Click Next to go to the image analysis window (Fig. 2) of the first selected folder.

Remarks

  • If the Select and draw option is required for more than one folder, analyze them separately.
    → In that case, click Previous and select only one subfolder.

  • If only one folder requires the Select and draw option, analyze it first.
    → To do so, deselect all folders, select the one that needs drawing, then hold Ctrl/Cmd while selecting the others.

  • If the first selected folder has already been analyzed, two shortcuts appear:

  • Video tracking window → skips the image analysis window, lets the user tune video tracking before running all
  • Run all directly → skips both image analysis and video tracking, applies saved settings to all folders directly