Release of v0.3.0

This release brings a lot of new tasks, features and general improvements. Amongst them are the following:

• Added W: Review annotine annotations (multi/merged) task that will enable generation outputs that can be used by the annotine-review app
• Added W: SHAP bubble plots (single/multi/merged) task which will automatically generate bubble plots for a set of classification outputs
• Added Distributions of ion centroids (single/multi/merged) task which lets you compare intensity distributions across samples/masks
• The Review GeoJSON masks from QuPath task can now generate directories compatible with multi-transformation/dataset approach (e.g. see Ally for issues why that might be useful)
• The error messages have been vastly rewritten and improved
• The layout has been updated to simplify creation of tasks
• There is now a button next to the Profile drop-down which lets you automatically populate the task list.
• Many tasks have had their defaults improved.
• Many tasks have had a number of parameters introduced for better controls.
• Many other fixes and improvements.

Release of v0.2.1

This is a bug-fix release.

Changed

• Slight changes to the UI
• Improved messages for reference datasets

Fix

• fix issue with app throwing errors in the mass-spectra and heatmap tasks

Release of v0.2.0

This is a substantial release with a lot of new functionality

New

• Complete revamp of the user interface, making it easier to edit tasks.
• Added Add reference project…` and Remove reference project… options to allow creation of ‘multi-project’ projects when dealing with a lot of data.
• Added `P: Create a merged project from a select single-datasets (merged-project) task, which will create a merged dataset based on your selection.
• Added P: Skyline mass spectrum (single-dataset) task, which will create a skyline mass spectrum (instead of average) - this can be used in any other task that uses mass spectra.
• Added Filter ion centroids (single-/multi-dataset), which will help reduce the number of isotopic ions from your peaklists.
• Added W: XGBoost training (single/merged-project) task, which is a more specialized supervised classification workflow that does multi-iteration training + SHAP.
• Added W: Annotate average mass spectrum (merged-project) task, which will provide annotations for the average mass spectrum of each dataset in a merged project.
• Added P: Normalization (merged-project) task, which will provide normalizations based on a subset of datasets.
• Added m/zs (must be used in calibration) to the calibration task. This will ensure that the RANSAC model used during calibration ‘overfits’ on the specified m/z. It is very useful when an internal standard or lockmass is used.
• Enabled automatic SNR detection for all Annotation tasks. This is based on a simple knee rule where we try to find optimal SNR based on the number of peaks detected. When knee is detected, SNR is assumed to be optimal.
• Added Enable filtering rules to all Annotation tasks. This will enable rules defined by Maddie.
• Added Group statistics of mass spectra and Group statistics of ion centroids which will enable generation of dataset or mask distribution plots.
• Added a Creating/Editing field to the statusbar to indicate which action is taking place.
• When opening a project, the retrieval of metadata information is performed in another thread, so it should no longer block the UI.
• There is now an option to disable instance validation, which substantially speeds up task addition. Tasks are always validated during export.

Changed

• Added a few extra adducts to the Annotation adduct selection (M+Ag, M+Li, M+H-H2O).
• The Quality control task has now been separated into W: Compute quality control metrics and W: Visualise quality control metrics to reduce the amount of data duplication.
• Separated export of the mass spectrum to a separate task due to a design flaw (stupidly, mass spectra were exported before calibration, which is not particularly helpful). If you want to have mass spectrum, please add E: Export mass spectrum task to the queue.
• Tasks are no longer appended to the end of the queue but rather inserted in the appropriate location according to their priority (execution order).
• Many of the tasks now have improved defaults.

Fixed

• Many small bugs.
• Even more big bugs.
• Filtering of tasks is better now.

Release of v0.1.11a0

This is an alpha release to fix a couple of bugs.

New

• When creating tags.csv file and a file already exists, you will be asked to confirm if it should be overwritten. If so, a backup will be created.
• Improved validation of P: Register GeoJSON masks from QuPath
• Added a couple of hints to nudge you to check the input data.
• Added more hyperlinks to the Notes / Warnings / Errors section so you can just click and be done with it!
• The polarity section of Directory contents is now clickable - helpful if you accidentally put positive & negative mode data into the same project and want to check what doesn't add up. (it would say mixed)

Changed

• Updated icons so that if it's a warning, it is a check mark since it does pass validation but might have some minor warnings.

Fixed

• Fixed a bug which happened if you tried saving settings with W: Mass spectral QC task in the list.

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.

Release of v0.1.8

What's Changed

New

• You can download the newest version of the app from within AutoIMS!
• Added new W: Compare spectra (one-vs-one, single dataset) task that will compare spectra within a single dataset
• Added W: Average mass spectrum / cluster (single-dataset) task which will let you generate average mass spectrum for each KMeans cluster (these can be used for comparing spectral differences and in the future, for annotations
• Added tSNE as an additional dimensionality reduction method
• Added a couple of parameter options to both W: Unsupervised tasks (mostly for UMAP)
• Added Find the optimal number of clusters option to the W: Unsupervised... tasks which will automatically determine the optimal number of clusters using the elbow method
• Added a button to validate against the data in the raw directory - a short report will be shown to say whether files in your raw directory are matched against the tags.csv file.
• Each time a task is missing some dependency (other task required), it will now display it as a hyperlink which you can click and be taken to the missing task.
• Added toggle between light and dark theme of the app
• Added option to export centroid data as image2image compatible HDF5 files (available to use in the next release of image2image
• You will be warned if there is no ion mobility data in the raw directory but you've selected W: 2d feature detection task
• Added a sort button to the selected tasks so you can sort tasks by their priority (it's automatically done when saving config but might be helpful)
• It is now possible to remove user from the M: Contact information task
• You will now have to confirm whether you want to close the window to prevent accidental losses of data

Removed

• Removed the Ex: Centroids to OME-TIFF, Ex: Centroids to Fusion CSV and Ex: Dataset to imzML tasks and migrated the export to the Wf: Extract ion centroids where you can select several export options (multiple exports permitted per task)
• Removed the Ex: Average mass spectrum task - it is now integrated directly into the Pre: Average mass spectrum task (multiple exports permitted per task)
• Removed the method=extracted from Ex: Dataset to imzML task as it's no longer needed here (see Wf: Extract ion centroids)

Changed

• Renamed the Wf: Compare spectra grid to Wf: Compare spectra (one-vs-one, multi-dataset).
• Moved the Profiles combobox to a new location so it occupies less space
• Changed the way we display paths to use hyperlinks so you can click on them and be taken to the right folder
• Renamed all tasks to no longer use the Pre or Wf identifiers - they are now P or W to make names slightly shorter
• The tag variable of W: Extract ion centroids can now be auto-generated
• Cleaned-up the results directory so fewer directories will be now created
• The icons indicating whether something is valid or not have been moved to the left-hand side
• There are now three different icons to indicate whether a task is valid. Those are succes (green check mark), warning (orange warning sign) and error (red cross). As before, warnings are simply there to notify you of some additional considerations but will not cause task failures.
• Logging is now much more extensive so hopefully that will help us catch bugs/errors.
• The automatically tags.csv will now feature much more reasonable defaults.

Fixed

• The Wf: Unsupervised training (multi-dataset) task now permits multiple instances (e.g. PCA and UMAP in the same config...)
• Fixed a bug which prevented manual filename creation
• Fixed many bugs in task validation
• Fixed a bug which prevented proper loading of tags.csv
• Pre-selected calibrants will now be properly selected in the Selection window
• Fixed a bug where the average mass spectra files always had an odd name
• Tutorial will no longer go backwards

Breaking Changes

• Hopefully nothing - configs from v0.1.7 will be automatically upgraded to latest schema version.
• Configs from previous versions might have some minor errors that need fixing

Release of v0.1.7

What's Changed

• added Wf: 2D feature detection (single-dataset) task which enables 2d feature detection
• added Pre: Merge single-datasets task which combines several datasets obtained from different files into one large dataset
• added Wf: Unsupervised training (multi-dataset) task - now that we can create multi-dataset objects
• added Tutorial that walks through various aspects of the app (shown on first initialization and can be found in the statusbar/menu)
• fixed automatic tags.csv file generation
• added progress bar to show the progress of generating automatic tags.csv
• added 👍 button to allow manual validation of tasks
• improved validation of filenames and tags
• improved validation of many tasks
• validation of the 'Available' and 'Selected' tasks is now slightly different
• duplicate filenames/tags are no longer permitted
• certain tasks will now not be allowed for centroids generated with different m/zs
• added more information about certain fields
• added style to annotation task
• improved layout/ui
• some logging information will now show in the main window
• the version checker background task will run slightly more frequently now
• fixed hundreds of little bugs

Release of v0.1.6

Yanked and re-released as v0.1.7

Release of v0.1.5

What's Changed

• Improve normalization defaults (e.g. selecting normalization task will auto-select it in other tasks)
• Improve data validation
• Fixed a bug where it was not possible to clear selected tasks
• Improved the way normalizations are validated
• Improved the way centroids are validated
• Fixed a bug where would be saved to the wrong place
• The average heatmap will now also produce average mass spectrum (which can automatically complete the average mass spectrum task)