Foci Analyzer v1.4

New in this release:

• Visualization/GUI improvements:

  • Added option to include foci outside nuclei/cells. The distance range can be specified.
  • Included option to detect foci on extended depth of focus projection (Sobel, GPU)
  • 3D image options are now radiobuttons instead of separate checkboxes
  • Downscaled nuclei masks are now smoothed using spline fitting (StarDist only)
  • If the 'Alt' key is pressed before a file is loaded, the user can select a ROI to do a preview analysis on.
  • Added a cellpose diameter parameter (was set to default (30 pixels) before)

• Output improvements:

  • The actually used threshold value (Threshold factor * bias) is now mentioned in the log window and added to the output image metadata.
  • Colocalization overlap image is now also 3D and saved as .Gif file to save space

• Bug fixes:

  • Fixed a bug causing a crash with 32-bit images when producing the overlay.

The macro Merge_result_files_1.1 (see below) can be used to merge all foci results .tsv files in a folder into a single table and .tsv file.

Foci Analyzer v1.3

New in this release:

• Visualization/GUI improvements:
  • Press & Hold 'Alt' before opening a file allows the user to select a ROI to do a preview analysis on.
  • Created 3D handling radiobuttons instead of separate checkboxes, and moved that to higher in the parameter dialog.
  • Added labels to the four channels in the overlay image.
  • Colocalization overlap image is now also 3D and saved as .gif file.
• Additional changes:
  • Downscaled ROIs are now smoothed using spline fitting.
  • Added an option to crop the image borders
  • Added total nucleus intensity (mean*area) as output column.
  • Threshold factor * bias is now mentioned in the log window.
  • Small bug fixes

Foci Analyzer v1.2

New in this release:

• Fixed critical bug where after threshold optimization of the second image Fiji would crash (because an image was released from the GPU)
• Improved log window readability
• Fixed a bug (in debug mode) where Fiji crashed after threshold optimization if the overlay image was not selected

Foci Analyzer v1.1

New in this release:

• Fixed a small bug: nuclear intensity in foci channel B is now measured also when detectFociChannelB is false.
• Changes in AreaMaximum detection (minimum foci size)
• Now asks to create output folder if it doesn't exist.
• Classic nuclei segmentation now works again
• Fixed a bug where the nucleus area was not correctly reported when Stardist nuclei binning factor > 1

Foci Analyzer v1.0

First release