Software

Fast4DReg (2023)

Fast4DReg is a Fiji plugin for 2D and 3D video and can correct drift in all x-, y-, and z-directions. Fast4DReg creates intensity projections along both axes, estimates their drift using cross-correlation-based drift correction, and then translates the video frame by frame. Additionally, Fast4DReg can be used for aligning multi-channel 2D or 3D images, which is particularly useful for instruments that suffer from a misalignment of channels.

Read our paper and find Fast4DReg on GitHub.

TrackMate (2022)

TrackMate is your buddy for your everyday tracking.

TrackMate is an automated tracking software that analyzes bioimages and is distributed as a Fiji plugin.

TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Read our article here.

Automated cell tracking using StarDist and TrackMate. Read our paper here.

See TrackMate in action here.

ZeroCostDL4Mic (2021)

ZeroCostDL4Mic allows the use of popular Deep Learning neural networks capable of carrying out tasks such as image segmentation and object detection (using U-Net, StarDist, and YOLOv2), image denoising and restoration (using CARE and, Noise2Void), super-resolution microscopy (using Deep-STORM) and image-to-image translations (using Label-free prediction fnet, pix2pix, and CycleGAN).

Read our paper and access the ZeroCostDL4Mic platform.

FiloMap (2019)

ImageJ and R scripts used to map the localization of proteins within filopodia and generate filopodia maps.
Read our paper here.

Step-by-step protocols on how to use FiloMap to compare the localization of multiple proteins within filopodia.
Access our article here.

Find FiloMap on GitHub.

FiloQuant (2017)

The filopodia quantification plugin

FiloQuant is a user-friendly tool for the automated detection and quantification of filopodia properties such as length and density. We developed FiloQuant as a plugin for Fiji. Read our paper.

Step-by-step protocols on how to use FiloQuant to quantify filopodia
and filopodia-like protrusions from microscopy images. Access our article here.

Find FiloQuant on GitHub.