Release of v0.1.10

What's Changed

New

• Added Compare mosaic images (single-dataset) task which will create grid of ion images for each dataset separately.
• Added Register GeoJSON masks from QuPath task which will co-register QuPath generated GeoJSON files with your IMS data
• Added Register image2image HDF5 masks tasks which will co-register masks generated in image2image (based on QuPath GeoJSON files)
• Added W: Average mass spectrum / mask (single-dataset) task which will use the co-registered masks for generating average mass spectra
• Added W: Annotate mass spectra (single-dataset) task which will provide annotations for each mass spectrum in dataset (e.g. spectra from masks or clustering). You can specify which kind of spectrum (or spectra) should be used.
• Added W: Supervised training (single-dataset) and W: Supervised training (merged-project) tasks which add supervised/classification training.
• Added W: Peak ion statistics task which let's you discover which m/zs are up- or down-'regulated' between groups of datasets. This uses a subset of pixels to estimate p- and q-statistics.
• Added W: Centroid ion statistics task which let's you discover which m/zs are up- or down-'regulated' between groups of datasets. This uses all pixels to estimate p- and q-statistics.
• Added W: Mass spectral QC task which computes quality control stats such as ppm error, peak resolution, etc for a subset of ions of interest.
• Added a field to enable filtering of tasks to quickly disable tasks that are not required.
• Added Create template and Check database options to the W: Annotate ... tasks to validate whether provided database files will be accepted by annotine.
• Added Masks selection to the W: Unsupervised... tasks, enabling you to focus the unsupervised training on a subset of pixels.
• Added Export to file to the W: Unsupervised... tasks, enabling you to export OME-TIFF or HDF5 files (which you can view in image2image!).
• Added image2image HDF5 export in the W: Extract ion centroids task.
• Added polarity check to warn you if you put in mixed polarity data.
• Added annotine database validator to make sure it can be read by annotine (check for column names in the CSV file).
• It's now possible to use different spectra/heatmap sources in the Feature detection tasks. This can help in finding more interesting features specific to a particular mask.
• It is now possible to use different spectra in the Annotation... workflows.

Changed

• The colormap dropdown is now searchable to speed things up.
• The Compare mosaic images (stitched) has been renamed to Compare mosaic images (multi-dataset)
• The Compare mosaic images (multi-dataset) will once again only support common peak lists.
• Renamed W: Annotate spectra (annotine) to W: Annotate mass spectrum (multi-dataset)
• Improved the walk-through tutorial with more information.
• Validation should be much, much faster now.
• Improved validation of nearly every task (please read the warnings!)
• Updated the list of annotine databases (removed HMDB4 and added LMSD).
• You can now select multiple Plot styles in all tasks that have that option. This let's you experiment with different plots.

Removed

• Removed the Grid/tags field from P: Tags and names task since it was not necessary.
• Removed the option to specify own Tag (identifier) from several tasks - they are now automatically generated.
• Removed the Method option from P: Mass alignment and P: Mass calibration tasks since it could lead to poor results if used incorrectly.

Fixed

• Fixed hundreds (thousands?) of bugs and inconsistencies.

Breaking Changes

• Hopefully nothing? Please let me know if you notice anything doesn't work as it used to.