Releases: BioImaging-NKI/Foci-analyzer
Releases · BioImaging-NKI/Foci-analyzer
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