ACQUIFER Fiji Utilities

ACQUIFER Fiji Utilities

Image processing by ACQUIFER

We provide several software tools on the ACQUIFER update site for Fiji (freely available upon request).

These tools are ideally suited for processing ACQUIFER Imaging Machine data (batch, metadata extraction) and for feedback microscopy workflows. They address common processing needs when handling multidimensional IM datasets and serve as building blocks for more advanced image analysis pipelines.

We also offer the development of custom image analysis solutions for Imaging Machine customers after assessment of your project. Ideally, we team up at early stage of assay development to balance imaging and analysis needs.

Contact us for further details and information!

Batch processing of IM data

GUI of the hyperstack plugin

Data annotation

Image annotations
  • Annotation of regions of interest, images or entire datasets
  • For routine analysis and ground truth annotation
  • Optimized for large datasets
  • Combined processing of regions of interest or entire images
  • Based on ROI 1-click tools and Fiji plugins for qualitative image annotations developed by us (Thomas et al. 2020, Thomas et al. 2021)
  • Video tutorials available (ROI 1-click tools, Qualitative Annotations)

Object detection

object-detection in zebrafish
  • Automatically locate regions and objects of interest
  • Broad applicability and compatibility with various samples and assay
  • Based on Multi-Template Matching developed by us (Thomas et al. 2020)
  • Video tutorials available on YouTube

Smart Imaging

smart imaging fiji plugin
  • Tools for feedback microscopy applications (e.g. pre-scan/re-scan)
  • Interface Fiji with the ACQUIFER Imaging Machine using IM script commands
  • Identification of regions of interest for subsequent centering and imaging
  • Built-in object detection based on multi-template matching, intensity features or expert annotation

For developers

scripting in fiji with the acquifer API
  • ACQUIFER Java packages for scripting in e.g. Fiji and other java software
  • Metadata parsing, batch execution…
  • See example macros/scripts in Fiji (menu ACQUIFER > Examples) or on GitHub
  • Experimental tools for more complex workflows
  • Support for previous IM versions (menu ACQUIFER > Legacy)