Fix Fixed catastrophic issue with app throwing errors in the mass-spectra and heatmap tasks
v0.2.0
New Complete revamp of the user interface, making it easier to edit tasks.
New Added Add reference project…` and Remove reference project… options to allow creation of ‘multi-project’ projects when dealing with a lot of data.
New Added `P: Create a merged project from a select single-datasets (merged-project) task, which will create a merged dataset based on your selection.
New 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.
New Added Filter ion centroids (single-/multi-dataset), which will help reduce the number of isotopic ions from your peaklists.
New Added W: XGBoost training (single/merged-project) task, which is a more specialized supervised classification workflow that does multi-iteration training + SHAP.
New 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.
New Added P: Normalization (merged-project) task, which will provide normalizations based on a subset of datasets.
New 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.
New 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.
New Added Enable filtering rules to all Annotation tasks. This will enable rules defined by Maddie.
New Added Group statistics of mass spectra and Group statistics of ion centroids which will enable generation of dataset or mask distribution plots.
New Added a Creating/Editing field to the statusbar to indicate which action is taking place.
New When opening a project, the retrieval of metadata information is performed in another thread, so it should no longer block the UI.
New There is now an option to disable instance validation, which substantially speeds up task addition. Tasks are always validated during export.
Change Added a few extra adducts to the Annotation adduct selection (M+Ag, M+Li, M+H-H2O).
Change 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.
Change 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.
Change Tasks are no longer appended to the end of the queue but rather inserted in the appropriate location according to their priority (execution order).
Change Many of the tasks now have improved defaults.
Fix Many small bugs.
Fix Even more big bugs.
Fix Filtering of tasks is better now. (edited)
v0.1.11
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.
New Improved validation of P: Register GeoJSON masks from QuPath
New Added a couple of hints to nudge you to check the input data.
New Added more hyperlinks to the Notes / Warnings / Errors section so you can just click and be done with it!
New 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)
Change 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.
Fix Fixed a bug which happened if you tried saving settings with W: Mass spectral QC task in the list.
v0.1.10
New Added Compare mosaic images (single-dataset) task which will create grid of ion images for each dataset separately.
New Added Register GeoJSON masks from QuPath task which will co-register QuPath generated GeoJSON files with your IMS data
New Added Register image2image HDF5 masks tasks which will co-register masks generated in image2image (based on QuPath GeoJSON files)
New Added W: Average mass spectrum / mask (single-dataset) task which will use the co-registered masks for generating average mass spectra
New 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.
New Added W: Supervised training (single-dataset) and W: Supervised training (merged-project) tasks which add supervised/classification training.
New 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.
New 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.
New 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.
New Added a field to enable filtering of tasks to quickly disable tasks that are not required.
New Added Create template and Check database options to the W: Annotate ... tasks to validate whether provided database files will be accepted by annotine.
New Added Masks selection to the W: Unsupervised... tasks, enabling you to focus the unsupervised training on a subset of pixels.
New Added Export to file to the W: Unsupervised... tasks, enabling you to export OME-TIFF or HDF5 files (which you can view in image2image!).
New Added image2image HDF5 export in the W: Extract ion centroids task.
New Added polarity check to warn you if you put in mixed polarity data.
New Added annotine database validator to make sure it can be read by annotine (check for column names in the CSV file).
New 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.
New It is now possible to use different spectra in the Annotation... workflows.
Change The colormap dropdown is now searchable to speed things up.
Change The Compare mosaic images (stitched) has been renamed to Compare mosaic images (multi-dataset)
Change The Compare mosaic images (multi-dataset) will once again only support common peak lists.
Change Renamed W: Annotate spectra (annotine) to W: Annotate mass spectrum (multi-dataset)
Change Improved the walk-through tutorial with more information.
Change Validation should be much, much faster now.
Change Improved validation of nearly every task (please read the warnings!)
Change Updated the list of annotine databases (removed HMDB4 and added LMSD).
Change You can now select multiple Plot styles in all tasks that have that option. This let's you experiment with different plots.
Remove Removed the Grid/tags field from P: Tags and names task since it was not necessary.
Remove Removed the option to specify own Tag (identifier) from several tasks - they are now automatically generated.
Remove Removed the Method option from P: Mass alignment and P: Mass calibration tasks since it could lead to poor results if used incorrectly.
Fix Fixed hundreds (thousands?) of bugs and inconsistencies.
v0.1.8
New You can download the newest version of the app from within AutoIMS!
New Added new W: Compare spectra (one-vs-one, single dataset) task that will compare spectra within a single dataset
New 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
New Added tSNE as an additional dimensionality reduction method
New Added a couple of parameter options to both W: Unsupervised tasks (mostly for UMAP)
New 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
New 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.
New 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.
New Added toggle between light and dark theme of the app
New Added option to export centroid data as image2image compatible HDF5 files (available to use in the next release of image2image
New You will be warned if there is no ion mobility data in the raw directory but you've selected W: 2d feature detection task
New 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)
New It is now possible to remove user from the M: Contact information task
New You will now have to confirm whether you want to close the window to prevent accidental losses of data
Remove 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)
Remove Removed the Ex: Average mass spectrum task - it is now integrated directly into the Pre: Average mass spectrum task (multiple exports permitted per task)
Remove Removed the method=extracted from Ex: Dataset to imzML task as it's no longer needed here (see Wf: Extract ion centroids)
Change Renamed the Wf: Compare spectra grid to Wf: Compare spectra (one-vs-one, multi-dataset).
Change Moved the Profiles combobox to a new location so it occupies less space
Change Changed the way we display paths to use hyperlinks so you can click on them and be taken to the right folder
Change Renamed all tasks to no longer use the Pre or Wf identifiers - they are now P or W to make names slightly shorter
Change The tag variable of W: Extract ion centroids can now be auto-generated
Change Cleaned-up the results directory so fewer directories will be now created
Change The icons indicating whether something is valid or not have been moved to the left-hand side
Change 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.
Change Logging is now much more extensive so hopefully that will help us catch bugs/errors.
Change The automatically tags.csv will now feature much more reasonable defaults.
Fix The Wf: Unsupervised training (multi-dataset) task now permits multiple instances (e.g. PCA and UMAP in the same config...)
Fix Fixed a bug which prevented manual filename creation
Fix Fixed many bugs in task validation
Fix Fixed a bug which prevented proper loading of tags.csv
Fix Pre-selected calibrants will now be properly selected in the Selection window
Fix Fixed a bug where the average mass spectra files always had an odd name
Fix Tutorial will no longer go backwards
v0.1.7
New added Wf: 2D feature detection (single-dataset) task which enables 2d feature detection
New added Pre: Merge single-datasets task which combines several datasets obtained from different files into one large dataset
New added Wf: Unsupervised training (multi-dataset) task - now that we can create multi-dataset objects
New added Tutorial that walks through various aspects of the app (shown on first initialization and can be found in the statusbar/menu)
New fixed automatic tags.csv file generation
New added progress bar to show the progress of generating automatic tags.csv
New added 👍 button to allow manual validation of tasks
Change improved validation of filenames and tags
Change improved validation of many tasks
Change validation of the 'Available' and 'Selected' tasks is now slightly different
Change duplicate filenames/tags are no longer permitted
Change certain tasks will now not be allowed for centroids generated with different m/zs
Change added more information about certain fields
Change added style to annotation task
Change improved layout/ui
Change some logging information will now show in the main window
Change the version checker background task will run slightly more frequently now
Fix fixed hundreds of little bugs
v0.1.5
Change Improve normalization defaults (e.g. selecting normalization task will auto-select it in other tasks)
Change Improve data validation
Change Fixed a bug where it was not possible to clear selected tasks
Change Improved the way normalizations are validated
Change Improved the way centroids are validated
Change Fixed a bug where would be saved to the wrong place
Change The average heatmap will now also produce average mass spectrum (which can automatically complete the average mass spectrum task)