ACQUIFER Fiji Utilities

ACQUIFER Fiji Utilities

Image processing by ACQUIFER

We provide several open-source tools that are ideally suited for processing ACQUIFER Imaging Machine data and for feedback microscopy workflows. These tools address common processing needs when handling multidimensional IM datasets and serve as building blocks for more advanced image analysis pipelines. ACQUIFER can also offer developing 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.

The ACQUIFER open-source tools are available as Fiji update site upon request. Contact us for further details and information!

Batch processing of IM data

  • Selective or batch access to multidimensional ACQUIFER Imaging Machine data.
  • Generation of hyperstacks and z-projections.
  • Batch processing using any application specific Fiji/ImageJ macro.

Data annotation

  • 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

  • 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 (link).

Smart Imaging

  • 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

  • Java package for ACQUIFER Imaging Machine datasets.
  • Macros and code examples.
  • Experimental tools for more complex workflows.
  • Legacy support.