- Add the ability to calculate absolute event counts (number of cells per microliter).
- Add the ability to automatically set scale parameters.
- Add the ability to download dose response fit information for multiple dose response plots at once. All selected dose response plots will now be included in the exported fit file.
- When pasting illustration objects between different experiments, CellEngine will now attempt to match FCS file and population selections by name.
- Annotations containing times now automatically sort properly.
- In the compensation editor, add the ability to view the plot for any channels, not just channels in the compensation matrix.
- Analysis algorithms now copy gates from the source experiment, aiding side-by-side comparison of automatic and manual population identification.
- Illustration chart Y axis labels now include the error bar type (standard error or standard deviation).
sorthas been removed as a standard API query parameter. It is now only supported where explicitly indicated in the API documentation. (This change affects API users only.)
- Quadrant and split gate labels now stay positioned at the corners of the plot when changing the channel scale.
- Add the ability to download a PDF containing only the selected components in an illustration.
- When in read-only mode, downloaded PDFs/PNGs of illustrations now reflect any changes that were made temporarily (without being saved). This includes the ability to change batch variables.
- Add the ability to download a spreadsheet of the information shown in the tailored gate inspection tool.
- Add the ability to create fine-grained Personal Access Tokens for using the CellEngine API. These are a secure way to provide a different, limited set of permissions to each API integration. For example, a file upload utility could be used with a token that only has the permission to upload files.
- Add the ability for domain administrators to send invitations to new users.
- Add the ability to see the edit history for annotations. Right-click on a cell and select "view edit history."
- Changed: When copying experiments, the audit trail now contains entries for the creation of all cloned resources.
- Changed: The standard deviation shown on statistics charts (such as line charts and bar graphs) has been changed from the population standard deviation to the sample standard deviation.
- The file selector in gating now remembers its sorting and filtering settings.
- It's now possible to copy and paste illustration images between experiments.
- All settings used to run algorithms are now shown on the experiment details page.
- When in per-file compensation mode, the current file's assigned compensation is displayed in parentheses for easy reference.
- To improve the appearance of gates, gate labels are now automatically repositioned to render within the plot, and gates shown in illustrations are clipped to the plot area.
- Add a percentile gating tool. This allows you to place a gate vertex at a percentile of the signal intensity of one or more corresponding control samples.
- Add the ability to copy and paste palettes in the color palette dialog.
- Add a column for the percent-of population's unique name in statistics exports.
- Add the ability to rename attachments.
- Allow creating “and” and “or” populations from other “and” and “or” populations.
- Add the ability for domain administrators to disable system-standard IAM roles, instead allowing only domain IAM roles to be used.
- Add the ability to select illustration components by type or styling.
- Add the ability to paste geometry to multiple gate simultaneously.
- Add the experiment path as a variable usable in illustration textboxes.
- Show the date that an attachment was uploaded in the attachments table.
- The t-SNE event limit has been raised from 5 million to 10 million events.
- Add the ability to specify the number of computed PCA components.
- Add the ability to specify which annotations, populations or channels map to which colors in illustrations.
- Allow creating folders within the folder selection dialog, when moving or copying experiments or folders.
- Show the definition of Boolean populations when hovering over them in the gating population hierarchy.
- Add the ability to customize color palettes in illustrations.
- Add the ability to copy and paste the position of individual gate vertices.
- When panels cannot be merged due to mismatched channels, list the mismatched channels when hovering over the merge-panel button.
- Support ctrl-clicking multiple options in the sorting dialog.
- The gating page now persists the selected channels, FCS file and population across page views.
- Add the ability to disable tooltips in illustrations via the View menu.
- The compensation editor grid is now colored by the matrix values.
- Add the ability to enable and disable per-file tailoring for multiple gates at once.
- Add the ability to cancel algorithmic analyses.
- Add the ability to change the thickness of histogram strokes.
- Add the ability to sign revisions when creating them.
- Add a tool to merge staining panels.
- Copies of experiments and experiments created by running algorithms now show links to their source experiments on the experiment summary page.
- Add Louvain (PhenoGraph), Leiden and Ensemble Clustering of Graphs (ECG) community-detection/clustering algorithms. CellEngine’s implementations can analyze up to 10,000,000 data points in about 15 minutes.
- Add the ability to take a screenshot when using the support request tool.
- Add the ability to import compensations in the Import Resources tool.
- Annotations created from filenames or file headers are now automatically created for subsequent file uploads and imports.
- Add a tool to inspect gate tailoring, accessible from the gating page.
- Add the ability to create linked gates.
- Add the ability to create “and” and “or” gates, and expand the scenarios in which “not” gates can be created.
- Add the ability to use the “apply tailoring” and “reset to global gate” tools for multiple populations at once.
- Add a warning when attempting to paste gate geometry between gates that use different channels.
- Use better default scaling for Cytek data.
- Add the ability to send gated or raw FCS files directly to an S3-compatible storage provider via the CellEngine API.
- Add the ability to sort and filter pages based on annotations in the page selector in batched illustrations.
- Add the ability to hide columns in file selectors.
- Changed: The
parentPopulationIdproperty has been removed from gates. It is now inferred automatically by CellEngine. This affects API users only.
- Add FlowSOM.
- Add the ability to omit pages with no matching files from batched illustrations.
- Add the ability to create combination populations.
- Add the ability to wrap text in columns in the annotation table.
- Add the ability to add comments to audit trail entries. This can help you explain why an action was performed.
- The “channel” variable in illustration textboxes is now replaced with the reagent name in addition to just the channel name.
- Add the ability to display the correlation between rows or columns in heatmaps.
- Add the ability to delete multiple populations at once.
- Add the ability to exclude ID columns from statistics exports.
- Add the ability to display file annotations as colored blocks adjacent to heatmaps.
- Add support for two-factor authentication.
- The settings used to run algorithms (i.e., t-SNE, PCA and UMAP) are now shown on the experiment details page.
- Add the ability to annotate experiments with structured metadata.
- The domain security event list now includes more types of events.
- Add the ability to import FCS files from S3-compatible providers, such as AWS. This feature is currently available via the API only.
- Add the ability to round exported statistics to a specified number of decimal places.
- Gates and their statistics are now shown in the compensation editor, making it easier to adjust compensation matrices based on population averages.
- Add the ability to move multiple values at once in the sorting dialog.
- Add the ability to concatenate FCS files from the annotation page. Previously files could be concatenated from the experiment summary page. This new interface makes it easier to select files to concatenate based on their annotations.
- When drawing gates, gate labels are automatically positioned so that they are inside the plot.
- Add the ability to flip bar charts and box plots horizontally and vertically.
- Add the ability to import compensation matrices from text files (including FlowJo’s format).
- The experiment summary page has been redone.
- The application header has been redone.
- The properties sidebar in illustrations has been reorganized and improved.
- Add the ability to import annotations.
- Add the ability to cluster and show dendrograms on heatmaps.
- All data table columns (e.g. FCS file tables) are now resizable.
- Compensation names must now be unique.
- The “prefilter” interface for pivot tables and charts has been simplified.
- PCA, t-SNE and UMAP are now available in closed beta. Contact email@example.com for more information.
- Add the ability to color dot plots by channel values.
- Add the ability to download compensation matrices as TSV, CSV and XLSX files.
- Add the ability to download file annotations as TSV, CSV and XLSX files.
- Add the ability to undo deletion of FCS files.
- Add the ability to right-click on a plot in illustrations and jump to that same plot in the gating interface.
- Add the ability to automatically mirror channels for rows and columns of pivot tables to facilitate making N x N visualizations.
- Add the ability to specify if pivot table channel dimensions apply to the X or Y axis.
- Add the ability to rename folders in the inbox subheader.
- Add the Viridis color scale option for heat maps.
- Add the ability to use an illustration’s batch variables for flow plot and pivot table Y-axis channels.
- Add the ability to cancel drawing a gate by hitting escape.
- Add the ability to add and remove channels from compensation matrices.
- Add the ability to paste gate geometry. This allows you to copy the shape of one gate and paste it to others.
- Add the ability to finish drawing polygon gates by double-clicking.
- Add the ability to overlay contour plots.
- Illustrations created by importing Diva workspaces now enable batched mode automatically.
- Add the option to show tick mark labels in gating.
- The inbox search field now supports searching experiments by path name, tags and comments. See organization and searching for more information.
- Change the sorting dialog to use population unique names.
- Change the inbox search to search all folders by default.
- Add a confirmation prompt to the “make orthogonal (all files)” action for quadrant gates.
- The Import Resources dialog has been redone. It now shows the folder hierarchy when selecting which experiment to import.
- The Import FCS Files dialog has been redone. It now shows the folder hierarchy when selecting which experiment to import.
- Change all compensation selectors to sort compensation matrices alphabetically.
- Enable editing multiple selected illustration components at once.
- Add a dynamic “all values” switch to illustration components. When files are uploaded or deleted, or their annotations are changed, components using "all values" will continue to include all of those files.
- Add the ability to search the channel selectors in illustrations.
- Plot type, palette and smoothing settings in gating are now persisted across sessions.
- Change the default smoothing for histograms and contour plots to 1 instead of 0.
- Add more heatmap color scale options.
- Change the “short-wide” statistics export layout so that it can be used in experiments with duplicate population names. The unique population name will be used in column headers.
- Add the ability to specify a destination folder when saving a copy of an experiment from the inbox.
- Add new features to the domain administration console:
- Add users to the domain.
- Remove users from the domain.
- Set password expiration.
- Enable/disable audit trail.
- Add support for folders as a way to organize and share your experiments.
- Add the option to connect gaps in line charts.
- Add the ability to skew quadrant gate lines.
- Tick labels in flow plots no longer overlap.
- Add the ability to right-click on a plot in illustration pivot tables and jump to that same plot in the gating interface.
- Add the ability to fill histograms with adjustable opacity.
- Add advanced Access Management. Most users will now see four sharing levels, described in sharing. Enterprise users can additionally use custom roles.
- Add audit trailing. Enterprise users can enable this for their domain.
- Add the ability to compare two revisions, or a revision with the current experiment state.
- Add the ability to copy or download the plot in gating.
- Add the ability to select the plot color palette in gating.
- Filenames-to-annotations now automatically strips the file extension.
- Add the ability to add and delete points from polygon gates.
- Show file annotations in the FCS file selector when importing files from another experiment.
- Add the ability to insert the current export time, current user’s name, illustration name and experiment name as variables in illustration textboxes.
- Add the ability to filter the annotation table.
- Add the ability to create “not” gates.
- Add the ability to manually resize annotation table columns.
- Change illustrations to use the experiment-wide compensation. Previously, compensation matrices were set for each illustration individually.
- Add the ability to filter date columns in the inbox.
- Add the ability to insert images in illustrations. Images can be inserted as separate components or inside of textboxes.
- Add a plot showing a live preview of scale changes to the scale editor.
- Add the ability to change scales for multiple channels at once in the scale editor.
- Add the ability to use keyboard arrow keys to step through files in gating. Click in the blank space of the file selector to enter this mode.
- Add an indicator that a gate is tailored to the gating page population hierarchy.
- Expand and refine the color palette in illustrations.
- Add the ability to tag experiments from the inbox.
- Add the ability to select whether to keep or replace existing annotations when using the annotations-from-headers tool.
- Add the ability to insert file annotations as variables into textboxes in batched illustrations when batching by FCS files.
- Add the ability to download PDFs of illustrations directly from the experiment summary page.
- Add the ability to save selections in the export-statistics page.
- Add the ability to import illustrations, accessible from the gating page.
- The “import populations” and “import scales” tools have been combined into a single “import” tool.
- Add illustration toolbar and menu buttons for zooming in/out. (These were previously only accessible via the keyboard, as +/-/0.)
- Add the ability to re-select the previously selected FCS files in the apply-tailoring-to dialog.
- Add the ability to filter the FCS file table in the apply-tailoring-to dialog.
- The FCS File selector in the batched illustration variables dialog now shows file annotations.
- Improve error messages that are displayed when attempting to upload invalid FCS files.
- Add the ability to hide gates in flow plots and pivot tables in illustrations.
- Add the ability to specify multiple “percent of ___” populations when
exporting statistics. Note: The response format for the
bulkstatisticsAPI has changed slightly to accommodate this change.
- Add the ability to specify a “percent of ___” population for bar charts, line charts, box plots, heat maps and dose response curves.
- Minor changes to illustration charts:
- The grid behind empty heatmap positions has been removed.
- The color scale in heatmaps is now limited to 200 px in height.
- The vertical line at x=1 in dose-response charts has been removed.
- Charts using “scale set” scaling now respect range overrides.
- Density and contour plots can now be rendered with a variety of color palettes.
- Bar charts, line charts, heat maps, box plots and dose response curves are now rendered in illustration PDFs and the native clipboard (e.g. when pasting into Microsoft PowerPoint).
- The experiment inbox now preserves your search, filter and sort state between navigations.
- Add the ability to download entire experiments as a single JSON file.
- Add contour plots.
- Add the ability to use batch variables for filter annotations in illustrations.
- Add the ability to rotate text boxes in illustrations.
- The experiment inbox can now be searched by experiment owner.
- Add the ability to subsample plots in illustrations.
- Add the ability to sign experiment revisions to indicate approval, review, or other meanings.
- Support for TLS 1.0 and 1.1 and weak cipher suites has been disabled to improve security.
- Add the ability to set retention policies on experiments to prevent them from being deleted for a period of time.
- Add the ability to define validators for FCS file annotation values.
- Add the ability to create batched illustrations.
- Histograms, tick marks and axes in illustration PDFs are now vector graphics, providing higher-quality images suitable for publication.
- Importing FCS files from other experiments now imports their annotations as well.
- Add the ability to filter the gating file selector.
- Histograms and density dot plots can now be smoothed using the "plot smoothing" controls in the toolbar.
- When exporting gated populations to a new experiment, the unique population name is now present as a file annotation.
- PDFs exported from illustrations now contain information about the experiment embedded in the file metadata.
- Resizing histogram overlays now also scales the offset between plots (pitch).
- Add event count and percentage statistics to the population hierarchy in the gating page.
- The annotation table interface has been revised for easier usage.
- Add the ability to specify a template for filenames when exporting gated populations.
uniqueName(the unique population name) to the population list API.
- Add the ability to customize axis ranges for bar charts, line charts, box plots and heatmaps.
- Show reagent names in the compensation editor.
- Populations, channels and FCS file names can now have custom sort orders. This allows you to adjust the layout of illustration pivot tables and charts that use populations, channels and/or FCS files as their row/column/table pivoting selections. Additionally, sort orders for the above and for annotations can now be specified on a per-illustration and per-illustration-component level, instead of only on an experiment-wide level. See annotation, population and channel sorting for more information.
- Heatmap colorbars can now be shown or hidden, and their tick font size can be changed.
- Dose response curve styling has been simplified:
- Error bars are no longer shown by default (but can be enabled in the sidebar).
- Hover text for the fitted curve has been removed
- The on-plot EC50 labels have been removed. (The EC50 and other fit information is still available by clicking on the fit line or clicking “download” in the sidebar.)
- The population hierarchy in gating has been redone to allow for faster interactions. In addition to the three-dot menu on the right side, population actions are now available by right-clicking on a population name.
- Quadrant and split gates are now enabled.
- Add the ability to add an “event number” column when exporting gated populations to a new experiment or downloading in a ZIP file. Additionally, via the API it is possible to add an “event number” column when downloading an FCS file as an FCS or TSV file and when creating FCS files from existing FCS files.
- Add the show-on-parent button to the row/column/table-level population selectors in pivot tables.
- Add the ability to hide labels at each level in pivot tables.
- Add the option to make pivot table labels “sticky.” When this option is turned on, labels will stay within the viewport as you scroll.
- When creating annotations from filenames, control files will no longer be automatically annotated.
- Add the ability to change the gate label font size in illustrations.
- When creating annotations from filenames, add the ability to merge new annotations with existing annotations. (For example, this allows you to use the filenames-to-annotations tool after uploading more files to an experiment that has already been annotated.)
- Improvements to illustrations:
- Add toolbar to align components relative to each other.
- Add Cividis color scale.
- Deleting the last character in a text box now preserves style settings.
- Text can now overflow the box.
- All text in PDFs exported from illustrations is now real, embedded text (that is, editable text that maintains a sharp appearance when resizing, instead of rasterized text).
- Channel selectors in illustrations now show reagents from all panels in the experiment.
- The compensation editor now opens with the channels currently displayed in the gating interface.
- Annotations with date values now automatically sort chronologically. See annotation sorting.
- Add the ability to paste a gate without its children. See copying and pasting gates for more information.
- Remove the limit on the number of source FCS files that may selected when downloading populations in a ZIP file.
- Add the ability to collapse empty rows and columns in pivot tables.
- Add the ability to import FCS files from other experiments.
- Add the ability to concatenate FCS files.
- Add the ability to save subsampled FCS files to the same experiment (currently accessible via API only). This is in addition to the existing ability to export subsampled FCS files/populations to a new experiment.
- Pivot tables now show the unique population name in cases where population names are not unique. (The unique population name includes ancestor names until the name is unique.)
- Improvements to pivot tables:
- Add the ability to make pivot tables with more than two dimensions by nesting tables.
- Add the ability to manually set label size.
- Add the ability to adjust spacing between rows, columns and tables.
- Add the ability to overlay columns (in addition to rows, as previously possible).
- Enable the show-on-parent button in the population selector.
- Add tall-skinny and short-wide statistics exports layouts.
- Add the ability to export Gating-ML for experiments.
- Show advanced information about CyTOF files (such as processing steps, CyTOF calibration and tuning data) in the file details dialog (accessible from the FCS file list on the experiment summary page).
- Add the ability to import scales from other experiments.
- Add the ability to extract FCS file annotations from file headers.
- Sort FCS files by filename in the experiment summary page.
- Add the ability to reset custom sort orders.
- Add a “uniquePopulationName” column to statistics exports. This value uniquely identifies populations that have the same name by including parent names until all names are unique.
- Add the ability to upload FCS files from the annotations page.
- Add the ability to delete non-consecutive rows and columns from the annotation table.
- Deleting an experiment now moves it to the trash folder, where it will be recoverable for about seven days before being permanently deleted.
- Add the ability to sort by multiple columns in the annotation page.
- Show the last time experiments were modified.
- Add the ability to select components in illustrations by clicking and dragging a box across the artboard.
- Add the ability to rearrange annotation columns.
- Add the ability to change FCS file filenames.
- Add the ability to apply gate tailoring by filename. Previously you could only do so by annotation.
- Downloading gated populations in a ZIP file is now faster, and interrupted downloads will automatically be resumed in supported browsers.
- Add the ability to subsample data when exporting populations.
- Show the current cursor coordinates in gating.
- Return more informative error messages for various types of invalid FCS files.
- Experiments in the inbox can now be right-clicked to display the context menu. (Most significantly, this lets you open experiments in new tabs.)
- Support left, right, center and justified text alignment in text boxes.
- Show the list of current user sessions from the user profile page.
- Add the ability to delete multiple FCS files at once.
- Add the ability to delete compensation matrices.
- Add the ability to export compensated FCS files with the export populations tool. See export compensated data.
- Improvements to bar charts, line charts, box plots and heat maps:
- Support normalization of data (e.g. fold change). See scaling and normalized plotting.
- Support Log2 scaling.
- Support both standard deviation (StdDev) and standard error of the mean (SEM). See replicate data, variability, error and error bars.
- Support a variety of color palettes for heat maps.
- Improve positioning of tick mark labels.
- Add the ability to manually adjust the sort order of annotations.
- Add the ability to view information about FCS files, such as laser delays and PMT voltages.
- Add X/Y channel swapping buttons to illustration flow plots and pivot tables.
- Add the ability to copy from illustrations to desktop applications (via ).
- Add the ability to copy and paste between different illustrations.
- Add the ability to display MAD, StdDev, CV and geometric mean statistics in gating and illustrations. Previously these were only available from the download statistics page.
- Add the ability to convert rectangle gates to polygon gates.
- If you attempt to upload duplicate FCS files to an experiment, you will be given the option to skip uploading duplicate files.
- Add bulk gate creation API. Up to ~1000 gates can now be created in a single API request.
- Improvements to Cytobank imports. See importing experiments from Cytobank
for more information.
- Imports now skip invalid FCS files instead of failing. A list of skipped FCS files will be included in the import notification e-mail.
- Populations will now be automatically created as necessary to make the hierarchy step-wise.
- Gates will now be automatically transformed from their per-gate scales to the experiment-wide scales.
- Tailored-per-population gates can now be imported.
- Gates that are not used in any populations will have a population automatically created below Ungated.
- Attempting to upload invalid FCS files now displays a more helpful message.
- Add the ability to tag experiments.
- Add the ability to change colors of lines, text box backgrounds and text box fonts.
- Add geometric mean statistic.
- Add per-file compensation.
- Add the ability to display the population name as the title of flow plots in illustrations.
- Add the ability to select the parent population to use in “percent of ___” statistics exports.
- Add the ability to reset a tailored gate to the global gate for a file.
- Add experiment revision system. Experiment revisions are ideal for clinical trials where auditable analyses are required.
- Add bulk FCS file annotation update API.
- Add the ability to change reagent names from the panels page. Previously this had to be done via the API.
- Text boxes and lines are now rendered in illustration PDF exports.
- Add the ability to toggle display of axis labels in flow plots and pivot tables.
- Parent population information is now always included in statistics exports.
- Add the ability to import BD FACSDiva experiments.
- Improved illustration PDF export.
- Add the ability to display pivot table column labels above or below tables.
- Add the ability to change pivot table axis label font size.
- Improve FCS file upload performance.
- Add the ability to select FCS files by name as rows/columns in illustrations.
- Add the ability to export gated populations to a new experiment.
- Improve visual clarity of gates and plots on high-DPI (“retina”) displays.
- Add the
createPopulationAPI query parameter to automatically create a population when creating a gate.
- Add the ability to download pivot tables and flow plots as PNGs.
- Add the
renderGatesAPI query parameter to render gates into plots.
- Add the ability to split filenames into annotations.
- Include channel reagents in statistics exports.
- Add show-on-parent button to population selectors in illustrations.
- CellEngine is now compliant with NIST 800-63 Digital Identity Guidelines.
- Support unitless dose-response curves.
- Support selecting populations via the population hierarchy throughout CellEngine.
- Redesigned compensation editor, including the ability to edit scales in tandem with compensation values.
- Add median absolute deviation statistic.
- Add histogram and dot plot overlays to illustrations.
- Improve autosorter behavior.
- Improve interactions in illustrations, including snap-to-grid and constrained resize.
And the rest is history...