Preprocessing

Overview

Preprocessing is an essential step to prepare your microscopy data for analysis in Celldetective. It includes both off-software and in-software methods to align, correct, and optimize your stacks for segmentation and downstream measurements.

Off-software preprocessing

Registration

We highly recommend aligning your movies before using Celldetective to correct for stage drift. This is typically done using external tools like Fiji (ImageJ).

See also

How to register stacks with Fiji for a step-by-step guide on using the customized Fiji macro for batch registration.

In-software preprocessing

The Preprocessing module lets you batch-correct stacks directly within Celldetective. Corrected stacks are saved with the prefix Corrected_.

Task	Description	Guide
Background correction (Model Fit)	Fits a 2D surface to the background, excluding cells. Best for fluorescence images.	how-to
Background correction (Model Free)	Computes a median background from multiple positions or timeframes. Best for brightfield/reflection microscopy.	how-to
Channel offset correction	Aligns channels that have pixel shifts between modalities.	how-to

For a full list of parameters (thresholds, tile options, etc.), see the Preprocessing Protocols Reference.

Bibliography

Schindelin, J., Arganda-Carreras, I., Frise, E. et al. Fiji: an open-source platform for biological-image analysis. Nat Methods 9, 676–682 (2012). https://doi.org/10.1038/nmeth.2019