Cytobank Release Notes

 

Dimensionality Reduction

TIME MATTERS: VISUALIZE YOUR RESULTS, FASTER

Statistical Interference

ALL IN ONE: FROM RAW DATA TO P-VALUE

Autocompensation

SIMPLIFY THE COMPENSATION STEP OF YOUR DATA ANALYSIS

Automatic Gating

REDUCE VARIABILITY AND SAVE TIME BY AUTOMATING YOUR GATING STRATEGY

Published on September 22nd, 2022

New Features

  • The Cytobank Automatic gating functionality allows the user to define a set of populations to be identified and the criteria for how they should be gated. Users can train a model on their data using their own panel and gating strategy. The trained model can be applied to files not previously analyzed – using the same panel – and can be shared with other users. Automatic gating can reduce the time needed for, and variability introduced by, manual gating.

Published on September 22nd, 2022

Changes

  • The stain index summary plot type now supports tailored gates (tailored by file, tailored by population, tailored by file and tailored by population).
  • Summary plot types configured with only a Population dimension now show data from all files for experiments with >25 experimental files.
  • The FlowSOM run info file no longer contains CSV files. To access statistical results of your FlowSOM run, please use the Export statistics tool.

Bug Fixes

  • Gate tailoring by population is retained for existing tailored populations after a gate is tailored to the Ungated population.

Published on June 13th, 2022

New Features

Functionality is added to the Automatic Compensation Wizard to offer more flexibility and control.

  • The new cleanup plot enables the user to select the events to be used for the spillover calculation. It consists of a dot plot with two user-defined channels and an ellipse gate that automatically adjusts to capture the events present in the plot. The user may tailor the ellipse gate per file to optimize the event selection. Use of the cleanup gate is restricted to the Compensation page.
  • Pairwise Compensation Plots provide a view to visualize the effects of the calculated compensation matrix on experiment files. Compensation sliders enable the user to adjust the compensation matrix.
  • Compensation matrices generated with the Automatic Compensation Wizard can be exported and imported for use in other experiments.

Changes

  • The Y axis of the single stain plots generated by the Automatic Compensation Wizard corresponds to the Y axis chosen for the cleanup plot.
  • The positive and negative gates for single stains generated by the Automatic Compensation Wizard can be adjusted by the user. The interactive positive and negative compensation gates are only available on the Compensation page.
  • When scale settings are adjusted, the user modifiable gates remain in the Automatic Compensation and can be manually adjusted to account for the change in population position.
  • Existing experiments that contain Automatic Compensation are updated to provide user-adjustable interactive gates.
  • Compensation sliders are added to the Preview Plot to enable the user to adjust the compensation matrix.

Published on May 23rd, 2022

New Features

  • The Connected users section of the user profile enables users to set a group of contacts with whom they can share experiments using the autofill functionality, share templates for illustrations and for exporting experiment statistics, and whom they can choose as PR or PI of an experiment or project. Users with prior access to at least one joint experiment or project will automatically be added to the Connected users list.
  • User connection requests can be sent to other users from the Connected users section in the user profile by entering a valid e-mail address. See the support article for details.

Changes

  • To improve privacy for users, EXIF metadata is removed from applicable image files when they are uploaded as attachment.
  • To share data with another user for the first time, the sharing user needs to send a connection request. This will make the sharing users username and e-mail visible to the recipient user. The recipient user needs to accept the connection request. The updated workflow of sharing experiments provides increased privacy and security. See the support article for details.
  • Populations defined by gates drawn on missing channels are shown as not applicable in the Illustration Editor and do not return ungated data.

Bug Fixes

  • Users are able to transfer tailored gates via cloning that splits files by population.
  • FlowSOM automatic cluster gates are generated for all metaclusters even when there are files missing some metaclusters.
  • UMAP and tSNE-CUDA no longer generate aberrant cross-shaped maps.
  • Median values for FlowSOM clusters are consistent between the export statistics function and the FlowSOM CSV result output.

Published on March 25, 2022

New Features

  • Updated backend architecture provides a more robust file upload, processing and download.
  • Upload and processing of large experiments is supported, e.g. 100 files with 3M events and 100 channels. Actual performance may vary based on experimental setup. Processing proceeds in the background for experiments created via ACS, *.zip files larger than 3GB and files uploaded through the DROP functionality that exceed 300 MB. Users are notified by e-mail about upload completion.
  • Note that this release results in changes to the Cytobank API. We have updated the API documentation accordingly./li>
  • An updated version of the CytobankAPI Wrapper for R will be made available.
  • An updated version of the Cytobank Plugin (version 1.2) will be made available.

Changes

  • When creating a new experiment via ACS file, the original ACS file is not attached.
  • Attachments need to be downloaded to be viewed and cannot be viewed in the Cytobank application.
  • Sample Tags must be downloaded from the Export menu.

Published on January 3, 2022

New Features

  • Summary charts are available in the Illustration Editor to visualize summary statistics for groups of samples based on user defined criteria. New charts types are: (stacked) bar charts, box and violin charts, line charts, summary dot and dimension-annotated heatmaps.
  • Automatic calculation and visualization of Stain index in the Illustration Editor.
  • Tests for statistical significance: (paired) Student’s t-test, Mann-Whitney U, Wilcoxon, One-way and Two-way ANOVA.
  • Multiple test correction.

Improvements

  • You will see saved illustrations after exporting CITRUS clusters showing a heatmap, a box chart showing event counts per cluster or medians depending on the selection for the algorithm run.
  • You will see saved illustrations after completed FlowSOM runs showing metacluster dot plot overlays in experiments containing dimensionality reduction channels, metacluster heatmaps and box charts visualizing overall population abundance for metaclusters.
  • User is able to select Percent of Population as Statistics in the Illustration editor.

Published on August 16, 2021

New Features

  • The Cytobank Dimensionality Reduction Suite is now available via the web browser and API. Users can now select from four dimensionality reduction algorithms to generate a two-dimensional categorized map representation of complex multi-parameter data sets.
  • The GPU-UMAP implementation of UMAP (Uniform Manifold Approximation and Projection for Dimension Reduction) is now available.
  • Users can now run tSNE-CUDA for a GPU-accelerated t-Distributed Stochastic Neighbor Embedding.
  • opt-SNE can now be selected for automatic parameter optimization.
  • The “Normalize scales" option enables users to scale each channel’s values to have a mean of 0 and a standard deviation of 1 for each of tSNE-CUDA, UMAP, and opt-SNE. Normalizing scales can be a useful strategy when channels have different dynamic ranges.
  • A new window in the Analysis Setup page allows for a direct comparison of results from different runs on the same dataset.

Improvements

  • Panel membership is displayed in the Channel popup window of the advanced analysis setup page to facilitate channel selection.
  • Channels used for advanced analyses are tracked and highlighted in the child and grandchild experiments.

Learn more about Dimensionality Reduction on the Cytobank Platform.

Published on January 18, 2021

New Features

  • Custom Colors are available for Overlays: When setting up dot plots and histogram overlays, you will be able to set custom colors including gray scale for files, populations, tags and plate dimensions. You can now control the opacity for histogram overlays from the plot settings menu.
  • Gates can now be applied via the API, enabling improved analysis pipelines and automated analysis strategies.
  • PLTNO FCS keyword can now be used to assign plate ID to determine which plate a file belongs to.

Improvements

  • You can now run viSNE on a subset of files that contain the same set of desired clustering channels. Files within the experiment that do not contain the clustering channels will not limit your ability to run viSNE when they are not selected. When setting up a viSNE run, all channels that are consistent across the selected files are available for selection.
  • When clicking on an experiment in the Experiment Manager, the experiment details load faster.
  • Copy a single plot or a complete Illustration from the Illustration Editor and paste it directly to office-type applications via your computer's buffer/clipboard. Use right click + copy or the Copy button in the hover menu for single plots or use the Copy button in the Export menu for the complete Illustration.
  • The character limit in the Project description was increased from 255 to 21332 characters.

Published on September 28, 2020

New Features

  • After upload or cloning without gates and annotations, users are directed to a new landing page that guides them through the next steps of the workflow (setting scales, compensation, and sample tags). Experienced users can opt to bypass this page and designate where in the app they’d like to land going forward.
  • Illustration Editor was re-designed with spatially intuitive controls to improve ease-of-use.
  • Illustrations are laid out and annotated in a more space-efficient, publication-ready format, with new controls for axis and annotation formatting.
  • The “Working Illustration” is no longer a concept; users can create “New illustrations”. Auto-save may be toggled on and off for illustrations.
  • Saved illustrations can now be edited, with “lock” controls to allow or prevent edits from other users with write access.
  • Users can clone illustrations as a basis for starting a new but similar illustration.
  • Populations now display in an interactive hierarchy in the Population dimension box; users can toggle in to “sort mode” to view them in list format.
  • Users can now define custom dimensions.

Improvements

  • Performance: illustration plots now load in a fraction of the time.
  • Illustrations automatically update without the user needing to click an Update button for most use cases (for very large illustrations, the user will be prompted to click an Update button).
  • Large illustration dynamics: users can Pause and Resume illustration updates; there are accurate % progress indicators for loading plots and statistics; the illustration layout is immediately configured (plots no longer jump around as they appear).
  • Enabled more control of illustration layouts and plot settings through direct interaction in line with plots.
  • Plot and layout settings can also be found in menus on the page-level navbar, which can be popped out to persist their open state. The layout menu allows users to configure rows, columns, and tables. An expanded Layout Editor is available to provide users with additional detail while configuring illustration layouts.
  • Users can now customize whether tables are laid out in rows or columns, including the new ability to have a series of rows (or columns).
  • Adjusted smart logic for default illustration layouts for FlowSOM-on-viSNE, viSNE, CITRUS export clusters, and plate experiments that defaults the initial layout to plot type, channel, and other illustration configurations commonly used in these workflows. The default illustration after first upload also now defaults to showing 3 Populations, 2 Channels, and 5 Files in a tabular view.
  • When first loading an illustration, the improved layout offers more space on screen for plots.
  • Font size of annotations better scales with size of plots.
  • Enhanced plot export: users can choose among SVG, PDF, and PNG formats for single plot or whole layout export. PDFs now faithfully mirror the illustration layout.
  • Export the illustration table of statistics to CSV using a button near the table; the format was updated to present values in columns, and significant digits were reworked to be more consistent with the rest of the application.
  • Pairwise plots was moved to the Templates menu and now renders as an illustration layout, giving users added control over what shows and exporting the results.
  • Gating Hierarchy was moved under the Gates menu and contains new controls for added flexibility in what displays and what users can export.
  • Export events and Split files by population no longer operate based on illustration settings; they have added controls and flexibility to govern output.
  • Split files by population is now located within the Cloning menu, giving additional power and flexibility.

Other updates

  • Users now define experiment-wide compensation (where applicable); compensation selectors have been removed from most pages in the application and functionality will now rely on the user-defined experiment-wide compensation.

Release Notes for Cytobank v7.3.0

Published on September 25, 2019

  • Security and infrastructure upgrades.
  • Additional bug fixes and minor improvements.

Release Notes for Cytobank v7.2.1

Published on August 16, 2019

  • Users can now clone experiments from the expanded detail section that appears when a user clicks on an experiment in the Experiment Manager.
  • The Updated value in the Experiment Manager is now influenced by descendant experiments Improvements to experiment nesting in the Experiment Manager.
  • The Experiment Manager now remembers users’ column visibility settings and pagination preferences.
  • The Inbox and Recent Tasks sections now show when viewing the Mine filter in the Experiment Manager.
  • The Group Linked feature is now available within Project pages.
  • Fixed a bug where PDF generation was failing with overlay plot types.
  • Additional bug fixes and minor improvements.

Release Notes for Cytobank v7.2.0

Published on May 1, 2019

  • The first view upon login has been rebranded as the Experiment Manager and provides a more performant and organized approach to managing and accessing your data. Learn more about the Experiment Manager.
  • A convenient experiment summary view now appears when clicking on an experiment from the Experiment Manager.
  • Linked experiments: advanced analyses and clones are now grouped under parent experiments in the Experiment Manager (this view is togglable). The family tree can be viewed from the Experiment Summary page. Learn more about linked experiments.
  • A section at the top of the Experiment Manager called the “Inbox” now appears if a user has a new, unviewed full-access shared experiment.
  • A section at the top of the Experiment Manager called “Recent Tasks” now appears if the user has any background tasks running or recently completed (FlowSOM, viSNE, SPADE, CITRUS, ACS generation, large exports).
  • A “Cytobank Curated” experiment filter was added, featuring public datasets curated by Cytobank.
  • Users can share experiments directly from the inbox (from the expanded details view).
  • Users can edit experiment names directly from the inbox (from the expanded details view).
  • Advanced analysis experiments no longer need to be cloned in order to run successive advanced analysis (e.g. running FlowSOM on viSNE).
  • Users can customize which columns show in the Experiment Manager, and settings are remembered.
  • Users can favorite or hide filters.
  • Users can rapidly view a list of experiments by Primary Researcher (for experiments to which they have access only).
  • Labels are now multi-colored, and colors can be changed by the user.
  • Clones are now listed on the Experiment Summary page.
  • An additional ACS export option was added, allowing users to export an experiment plus all of its descendants (children, grandchildren, clones, etc).
  • Advanced analysis experiments are now named the same thing as the algorithm run name.
  • SPADE child experiments are now unhidden/accessible, enabling users to work with resulting SPADE files that have cluster IDs written in.
  • The sign-up and self-payment workflow have usability improvements.
  • Project names are no longer shown to users without full access and non-project members for public experiments.
  • The Experiment Manager header is fixed while scrolling.
  • Users can search by filter queries such has “is:mine has:viSNE PBMC” in the search bar.
  • Counts for advanced analyses in the Experiment Manager now only reflect successful runs.
  • Full dates are now displayed in the Experiment Manager.
  • New users to Cytobank see an alternate “Create New Experiment” button that is called “Upload data and create new experiment”.
  • Users can specify a custom “Source” for an experiment.
  • Showing/hiding the New User Tour button that appears in the Working Illustration is now configurable via the user profile page instead of the Help menu.
  • New font site-wide, and various style improvements.
  • Bug fixes and minor improvements.

Release Notes for Cytobank v7.0

Published on November 27, 2018

  • FlowSOM is now available (via the web browser and API): Speed your time to analysis and quality of clustering with self-organizing maps that can reveal how all markers are behaving on all cells, and can detect subsets that might otherwise be missed. Learn More about FlowSOM..
  • Automatic Cluster Gates: new functionality in the gating interface to automatically draw gates around clusters. Learn More about Automatic Cluster Gating.
  • Advanced analyses are now grouped under an Advanced Analyses navbar menu (FlowSOM, viSNE, CITRUS, SPADE).
  • Performance improvements (inbox, histogram overlays, general plots & stats).
  • Support for viewing attachments within the browser from the Experiment Summary page (jpg, pdf, gif, png, txt).
  • Added pagination to the inbox.
  • The inbox now remembers the last filter selected.
  • Enabled import of gates from viSNE and FlowSOM experiments.
  • Bug fixes and minor improvements.

Release Notes for Cytobank v6.3.2

Published on September 6, 2018

  • Security enhancements.
  • Bug fixes and minor improvements.

Release Notes for Cytobank v6.3.1

Published on July 18, 2018

  • Cancel SPADE, viSNE, and CITRUS runs in progress to correct mistakes or refine settings.
  • Storage space used is now visible, and experiments can now be filtered by size in the inbox.
  • Improvements to cloning and sharing:  (Learn More).
  • Select which components from your experiments to clone, including:
    • Sharing permissions.
    • Project membership.
    • Illustrations.
    • Compensation matrices separately from gates.
    • Panels separately from sample tags.
    • Choose whether to give PI full access when experiments are cloned.
    • All cloning features are also supported by the API.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v6.3.0

    Published on May 3, 2018

    • Users can achieve reproducible viSNE results by setting the seed (via UI or API) — Learn More.
    • Gate name is now available as an option for display next to gates — Learn More.
    • Up to 8x faster rendering of illustrations.
    • Smart defaults added for scaling of Cytek Aurora files.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v6.2.1.2

    Published on March 12, 2018

    • Security patch for SAML / SSO.
    • Performance improvements.

    Release Notes for Cytobank v6.2.1

    Published on February 22, 2018

    • Accounts with evidence of multiple users sharing one account will be automatically inactivated by the application for violation of Terms of Service.
    • Upgraded the GatingML import UI module.
    • Added experiment count to the user profile page.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v6.2

    Published on January 18, 2018

    • Export stats UI enhancements: users can multi-select across boxes, drag & drop sorting.
    • New statistics available: Percent of Population and Event Count Ratio.
    • Export stats templates available for sharing among users and across servers, if desired (and admins can make templates public).
    • Users can now import scale settings from existing experiments.
    • Site administrators will be emailed weekly with list of users pending validation.
    • Implemented default scaling for the new debarcoding parameters (bc_separation_dist and mahalanobis_dist).
    • reCAPTCHA upgrade for smoother experience and higher security.
    • Improvements to ACS transfer.
    • Improvements to gatingML import for fluorescence data.
    • Updated Terms of Service for Premium and Community.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v6.1.2

    Published on November 10, 2017

    • Faster viSNE runs - up to 60% improvement in run times.
    • Faster loading of Manage Users and Advanced Analysis admin pages.
    • ACS transfer improvements.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v6.0

    Published on August 7, 2017

    • DROP functionality for converting spreadsheet files to FCS for analysis within Cytobank.
    • Improvements to default data scaling and the scale editor.
    • All dropdown menus are now searchable.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.6.1

    Published on April 13, 2017

    • Added support for perplexity, iterations, and theta to viSNE API endpoints.
    • Added API endpoint for downloading SPADE GML files.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.6.0

    Published on March 1, 2017

    • Redesigned and improved panel setup page: Configure panels, annotate channels, and resolve conflicts quickly and easily on the new panel setup page.
    • Improvements to file processing after upload to more intelligently group samples into panels with similar channel names.
    • New functionality to streamline process of accepting or rejecting user registrations on Enterprise Cytobanks (admin only).
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.5.0

    Published on January 3, 2017

    • API support for launching viSNE, SPADE, and CITRUS: Automate workflows and get even more done with the Cytobank API.
    • Added basic API endpoints for batch addition and removal of sample tags, adding and removing full access users (sharing), and uploading a compensation CSV file.
    • Illustration SVG Export: Export complete illustrations or individual plots as SVG for crisp labels that can be directly edited.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.4.1

    Published on November 7, 2016

    • More Power and Flexibility with viSNE: Increased event sampling cap to 2 million events, and exposed the ability to tune iterations, perplexity, and theta for better optimization of viSNE runs. (Learn more).
    • Overlay Enhancements: Easily visualize dozens of overlaid populations or other experiment variables with our new expanded palette of 64 colors.
    • Smarter scale defaults for FCS files from the Attune and YETI/ZE5 instruments.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.4.0

    Published on September 30, 2016

    • CITRUS: a high-dimensional clustering algorithm that automatically highlights statistical differences between sample groups and identifies predictive biomarkers.
    • Security enhancements.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.3.0

    Published on June 23, 2016

    • APIs: Enable programmatic access to Cytobank for your custom workflows.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.2.0

    Published on May 6, 2016

    • Ability to tailor gates across populations (TPP).
    • Gating rearchitecting, performance improvements, and bug fixes.
    • SPADE biaxial plot / compensation selection propagates more smoothly.
    • Experiment details page improvements (allow carriage returns in comments & purpose fields; directly edit details on page or in the drop down).
    • viSNE now supports FCS 2.0 files.
    • Site indicates if request to update an illustration has crashed instead of failing silently.
    • New illustration update requests cancel any pending requests (performance).
    • Performance improvement to “import illustrations” functionality.
    • Security enhancements.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.1.1

    Published on November 30, 2015

    • Single Sign-On follow-ups (Enterprise Cytobank only).
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.1.0

    Published on September 25, 2015

    • A guided, interactive analysis tour for new users that can be launched from the Working Illustration.
    • Support for Single Sign-On (SSO) integration with institutional Identity Provider (IdP) using SAML 2.0.
    • Gating Usability improvements, including an axis flipper and Population Manager filters.
    • Performance improvements (page load time for gating, tagging, and compensation).
    • viSNE now supports FCS 2.0 files.
    • Population Sunbursts can now be opened in Print View for SVG export.
    • Added a plot into the pop-up scale editor for increased usability, and added Active Population selectors for the scale editor and compensation plots.
    • Added filters and jumpers to project pages for increased agility when experiment hopping.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.0.1

    Published on July 24, 2015

    • Projects are sorted alphabetically.
    • Augmented our data backup service.
    • Introduced support for experiments with FCS files that have mismatched channel indices.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v5.0

    Published on June 12, 2015

    • Sweeping, site-wide improvements to navigation (improves usability and time to goal).
    • Compensation workflow improvements, including plot next to editable matrix, and auto-fill of positive/negative control assignments.
    • User can now self-service their subscriptions via credit card billing.
    • Performance improvements (inbox is 2x faster, illustration plots appear sooner, background tasks complete 4x faster, file downloads are prepared more quickly).
    • Gating hierarchy improvements.
    • viSNE runs are now included in ACS experiment packages.
    • Added hotkeys that allow users to quickly perform navigation actions or draw gates.
    • Added a print view to SPADE, Population Tree, and Gating Hierarchy.
    • Routine security enhancements.
    • Getting Started boxes are now accessible by clicking the page title or the question mark near the page title.
    • Dot Overlays and Histogram Overlay – Color by Row are now available on Community Cytobank.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v4.2

    Published on February 28, 2015

    • Added a new plot type (Dot Overlay) where users can overlay dot plots; any figure dimension can be overlaid! Complete your viSNE workflow or back-gate traditionally.
    • Added a fill option for Histogram Overlays called “Overlaid Figure Dimension” that allows users to color rows uniquely.
    • Added Plot Settings Templates, which allow users to save their favorite Working Illustration plot settings for ready access within any experiment.
    • Admins can make site-wide templates that will be available to all site users; set a “figure style” for your group!.
    • Reworked the Working Illustration plot control menus to be more usable, including consolidating to four parent Plot Types.
    • New hover tips help users better understand a functionality upon mouse-over.
    • The gating interface now has shapes in place of text on buttons, and Saved Illustrations show a handy plot type icon next to the name.
    • Improved the informative error output for histogram and dot overlay errors (layers, missing files).
    • Added a new beta functionality called “Simple Print View” that directly mimics the Working Illustration layout.
    • Added “Green to Red” as a Histogram Overlay – Gradient Color Set option.
    • viSNE and SPADE performance improvements.
    • Cloning time performance improvements.
    • Architectural upgrade (Rails 3).
    • New Experiment from Gated Files is now a background task for large experiments.
    • Improvements for Billing Admins.
    • Improvements to ACS file generation and upload.
    • Admin panel and architectural framework for cloud-based data transfer (by request).
    • Minor web API improvements.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v4.1

    Published on December 21, 2014

    • viSNE setup page improvements for large runs.
    • Security enhancements.
    • Admin tool: separation of users and Cytobank staff into tabs.
    • Minor improvements and bug fixes.

    Release Notes for Cytobank v4.0

    Published on November 14, 2014

    • viSNE: a dimensionality reduction algorithm (Premium Functionality).
    • Option to color dot plots by channel (Premium Functionality).
    • ACS import/export now gives user option to include SPADE trees.
    • Usability and improved look and feel.
    • Credits have been removed for Premium and Enterprise sites.
    • Bug fixes and minor improvements.

    Release Notes for Cytobank v3.2.2.1

    Published on August 5, 2014

    • Fix for Chrome-specific problem with rendering population trees.
    • Improvements to population ordering in the population tree.

    Release Notes for Cytobank v3.2.2

    Published on July 17, 2014

    • OpenID has been disabled as an authentication method; OpenID users must follow steps to convert their accounts to password-based login.
    • Billing enhancements.
    • Improvements to “Import experiment variables” functionality.
    • Added an informative “Site is down, be back at a schedule time” page when Cytobank is down for maintenance.
    • Miscellaneous bug fixes.

    Release Notes for Cytobank v3.2.1

    Published on June 27, 2014

    • For a large subset of conditions, SPADE runs that are unable to complete now display informative output about the reason for the failure and provide actionable steps to guide successful retry.
    • SPADE updates (handling files with blank reagent names, handling experiments whose files have different numbers of channels, enhanced handling of tree loads for large analyses, removed node merging).
    • Export statistics improvements (channel multi-select, window resize, instant processing for small runs).
    • Admins can now edit a user’s email address.
    • Security updates (email verification link now https, “Last logged in” field added to manage users page, passwords now require a minimum of 8 characters).
    • Other stability and general improvements.

    Release Notes for Cytobank v3.2.0.3

    Published on June 5, 2014

    • Security enhancements: workflow updates to user validation and email verification.

    Release Notes for Cytobank v3.2.0.1 and v3.2.0.2

    Published on May 28, 2014

    • Enhanced handling of SPADE runs that compute raw fold changes for trees with empty nodes.
    • Augmented sunburst and population tree statistics auto-refresh.
    • Additional error tracking tools.
    • Augmented handling of SPADE in Safari web browser.

    Release Notes for Cytobank v3.2.0

    Published on May 20, 2014

    • Sunburst visualizations (premium functionality) – a new way to visualize population hierarchy relationships and statistical information, found in the “Population Sunburst” tab in the gating interface.
    • Added event counts, percent of parent, and percent of total statistical information next to populations in the Population Tree in the gating interface.
    • Enhancements to error tracking to facilitate bug fixes.
    • Privacy policy updates in conjunction with error tracking.
    • Enhanced support for FCS 3.1 files.
    • Backwards compatibility for saved Export Experiment Statistics templates generated prior to Cytobank 3.0.
    • Added a “Notes” field to the billing interface for billing admins.
    • Enhancements to filter boxes within figure dimensions and the gating interface.
    • Manage Users admin page now indicates if a user is OpenID or username/password method of login.
    • Improvements to how the population tree mimics the gating hierarchy relationships.
    • Users are no longer prompted to login twice successively under certain session timeout conditions.

    Release Notes for Cytobank v3.1.0.1

    Published on April 30, 2014

    Following upgrade to 3.1.0 (FCS File Quality Validator), a few users reported upload failures that we determined to be caused to users’ web browsers relying on outdated cached contents. This release ensures that users’ web browsers are loading the updated content and not pulling from cache.

    Release Notes for Cytobank v3.1.0

    Published on April 22, 2014

    We have deployed our new file quality control (QC) module, where we provide more information to customers about how their files support the standard specifications set forth by the International Society for Advancement of Cytometry (ISAC). Errors in FCS files have become a growing concern at Cytobank as we have seen an increase in the number of ways FCS files are generated and the availability of several preprocessing tools which may not fully support the FCS specification proposed by ISAC. Files that do not meet the specification may affect how certain algorithms inside and outside of Cytobank interpret these files (e.g. SPADE can be affected by a bad file). The goal of the QC module is to let users know about problematic FCS files and inform the user about recommended changes/next steps. In most cases, discrepancies due to software are minor and do not affect end user analysis (if an experiment has such files, the discrepancies will be available to the user by clicking on the show warnings link).

    This update contained the following changes:

    • Detection and flagging of FCS files that do not conform to ISAC specification.
    • Knowledge base articles advising users how to proceed with flagged FCS files.
    • Additional support for uploads occurring with transient and inconsistent internet connections.
    • Bug fix for SPADE download PDF progress bar.
    • A fix to Experiment Comments and Purpose versioning.

    Release Notes for Cytobank v3.0.3.1, v3.0.3.2, v3.0.3.3

    Published on April 22, 2014

    • A bug fix to allow users to move gate percentages on experiments that were pre-existing prior to gating conversion (Cytobank 3.0 upgrade that removed Java).
    • Enhancements to the stability of the gating interface and error detection.
    • Enhancements to file upload, including support for transient and inconsistent internet connections.

    Release Notes for Cytobank v3.0.3

    Published on February 3, 2014

    This release contained 57 updates, including the following new functionality, improvements, and bug fixes:

    • Added new templating functionality that allows users to import or export saved illustration templates to and from experiments.
    • Users can now generate untransformed as well as transformed fold change calculations of SPADE results.
    • Export Experiment Statistics now offers “Tall” versus “Wide export formatting.
    • SPADE tables of statistics are now available in Download Analysis Data.
    • Email notifications are now sent when export statistics finishes.
    • Projects are now alphabetized on Create Experiment and Edit Experiment pages.
    • Users can now rename the export events zip file name.
    • Polygon gate line is now visible when drawing the gate before setting the point.
    • OpenID users who click “Forgot Password” are now notified that they don’t use a username / password method of login.
    • Enhanced usability of the Import Gates box.
    • Fixed issue with gate percentages labels being slightly offset in Working Illustration compared with the gating interface.
    • Fixed a bug where users with blank location or organization fields weren’t receiving email verification or password retrieval emails.
    • Fixed an issue with background tasks not starting occasionally (SPADE, exports).
    • Export events now features the option to include/exclude header with FCS Filename and to select which channels are exported.
    • Fixed an issue with SPADE bubble exports.
    • Classic Mac (CR) line endings are now handled correct for import experiment variables.
    • The new release has been thoroughly tested and is already on your servers but if you or your users notice anything amiss, please don’t hesitate to contact us.

    Release Notes for Cytobank v3.0.2.1

    Published on February 19, 2014

    • Added multiple styling options for histograms, including ability to customize histogram outline color, fill color, baseline, and spacing of overlaid histograms.
    • SPADE upgrades, including the ability to run SPADE on SPADE output files, per-file percent downsampling, statistics included in Download Analysis Data, and improved clustering (rclusterpp).
    • Security enhancements, including password expiry, password length requirements, requiring email verification, and configurable session timeout.
    • Several bug fixes to improve product performance and stability.

    Release Notes for Cytobank v3.0.1

    Published on January 28, 2014

    • Additional support for FCS files with special characters.
    • Additional support for duplicate-named FCS files.
    • Added Chrome Frame support for IE users.
    • All images, videos, and links updated to use https.
    • Offset of the population tree adjusted for better readability.
    • Support for users running SPADE on large experiments (>500 MB).
    • Gravitar image changed to silhouette of a user.
    • Warning added for users attempting to run SPADE on an experiment with log scales.
    • Ability to edit column header names for export statistics module.
    • Better handling of adding thousands of files to the uploader simultaneously.
    • Metal names and short names now both appear in SPADE PDF.
    • Bug fixes related to recent upgrade of gating, upload, and download.

    Release Notes for Cytobank v3.0

    Published on January 17, 2014

    Last week, we finished rolling out Cytobank 3.0, which retires the old gating, upload, and download applets and invokes a speedier, more widely-compatible HTML5-based infrastructure for these activities. Read our recent blog post for details.

    Release Notes for Cytobank v2.7.4

    Published on September 13, 2013

    • We’ve rolled out the latest release to all of our servers, and have a few changes we would like to highlight. First, links that are admin only now have a small wrench image next to them. These are functions that only admins on our servers have access to, including tools that are beta and may not yet be released. Second, the way SPADE and exports are handled in the background have improved. This means that several SPADE runs and exports can run in the background at the same time. Finally, if you migrate your old Cytobank data sets to a new server, ACS files (an archive of your entire experiment) will maintain their created date. This will help users keep track of older versus newer experiments regardless of when it was uploaded to the new server.
    • Minor Bug Fixes.

    Release Notes for Cytobank v2.7.3

    Published on July 9, 2013

    We’ve recently released Cytobank 2.7.3 which includes a new interface for exporting statistics. It is now possible to specify which stat, annotation, or keyword will be written to a .tsv or .csv file, and in what order. In addition, it is also now possible to save templates of often used statistics and load them between experiments for more efficient and consistent analysis. This new interface can be accessed by everyone via the “Export Experiment Statistics” link in the Actions toolbar while viewing the experiment overview.

    Release Notes for Cytobank v2.7

    Published on April 18, 2013

    We’ve incremented to the next sub version (2.7) with the release of our visual plate annotator interface, which allows users to lay out and annotate their plate-based experiments in a visual interface that mimics the actual plate used during sample acquisition. This manner of spatially arranging samples is aimed to facilitate high throughput annotation, and there are tools built in that are designed to facilitate annotating in patterns within and among plates. This functionality can be accessed through any of our premium functionality servers including DVS Cytobank and Enterprise Cytobank.

    Release Notes for Cytobank v2.6.2

    Published on February 22, 2013

    This release is largely comprised of functionality enhancements and stability improvements to SPADE, but also includes some features and fixes to general Cytobank functionality as well.

    New Functionality

    • Copy SPADE trees.
    • Download annotated SPADE trees.
    • Pop-out multiple biaxial plots from the SPADE tree viewer to view more than one 2D plot at once.
    • Select multiple bubbles.
    • Node size slider: adjust how node size is reflected visually.
    • Edit the name of Saved Illustrations.
    • Server admins are notified when MOTDs posted (maintenance messages).
    • Helpful support materials added to green.
    • Getting Started box on Dose Response Analysis page (DVS and Enterprise Cytobank).
    • Cleaned up and reorganized SPADE tree controls.
    • Hovering over a SPADE node now displays event count in addition to ID number.
    • Updated the upload applet.
    • Users can now only select one SPADE population (radio buttons instead of check boxes).
    • Upload applet allows users to select files now (not just folders).
    • Added a date “Updated” field for SPADE trees.
    • When public-access-only users make changes to a SPADE tree, they can click “Reset Visualization” and the tree will return to the last saved version.
    • Updated support text for the green Getting Started box within the SPADE tree viewer page.
    • Upgraded the download files client.

    Bug Fixes

    • Fixed the “Shared with me” Inbox filter on DVS Cytobank.
    • Changed “Target number of clusters” to “Target number of nodes” in SPADE setup.
    • Fixed an issue where users could end up with negative credits when cloning experiments.
    • Fixed a bug where tooltips (info buttons) were broken.
    • Fixed a bug where outer figure dimension labels were not appearing when an odd number of figure dimensions were enabled for standard plot views (non-heatmap, non-overlay).
    • Fixed broken links in export success email.
    • Fixed a bug where removing a selected node from a bubble sometimes failed for SPADE trees.
    • Fixed a bug with selective clone that was bringing over more channels than indicated.
    • Stability improvements to SPADE.
    • Node selections persist when users flip through samples.
    • Layered SPADE bubbles are no longer hidden.
    • Blue-yellow color scale for SPADE tree now matches that in the Working Illustration.
    • Changing SPADE analysis name now updates the name in the header bar.
    • Select all nodes now populates the table of statistics.
    • Exporting SPADE bubbles to a new experiment now consumes 1 credit (Enterprise servers).

    Release Notes for Cytobank v2.6-1-2

    Published on January 7, 2013

    New Functionality

    • You can now generate and download annotated PDFs for SPADE analyses.
    • Performance upgrades for working with tailored gates.
    • Plot Statistics render more quickly.

    Bug Fixes

    • Tooltips were broken; now they are fixed (in other words, dwelling your cursor over the “i” on a frame header brings up a popup window with support information).
    • All changes to SPADE settings trigger the save button.

    Release Notes for Cytobank v2.6, 2-6-0-2, 2-6-1, 2-6-1-1

    Published on November 2, 2012

    The big news from the release of our Cytobank 2-6 series is that SPADE is now available on our premium servers. Our developers have been hard at work enhancing the functionality over the past few months and we have been corresponding with early adopters to learn and implement their feedback. Dose Response Analysis is also now available on premium servers and will allow you to plot dose response curves and compute EC50 values for your titration data.

    New Functionality

    • SPADE is available on premium servers (Enterprise Cytobank and DVS Cytobank).
    • Dose Response Analysis is available on premium servers.
    • Exports now happen in the background and a zip file is created and attached to the Experiment Details page.
    • Export and Import experiment variables allows you to upload/download a spreadsheet of your annotations to further automate the annotation process.
    • SPADE autosave happens more frequently.
    • SPADE analyses can now be renamed.
    • Alphanumeric sorting is now available in the dimension boxes.
    • We now have a note on IE that SPADE does not work on IE.
    • There is now a warning on Windows 7/IE9 that the gating applet does not work.
    • Compensation can now be used in SPADE analysis generation.

    Bug Fixes

    • Other users in a shared experiment can see SPADE trees.
    • Fixes to accommodate long SPADE runs without marking them as defunct.
    • SPADE handles DiVa files.
    • Fixes to IE9 navigation.
    • Sharing an experiment now properly sends a notification email.
    • “Save and Return” goes to working illustration (cookies issue had redirection to Experiment Details page).
    • Fixed link in export success email.
    • When “Show Gates” is active, the “Show Gates” statistic drop-down menu is now active (was temporarily broken).
    • Some view-through plot bugs were fixed.
    • Pop-up support tips are not better formatted.
    • Default channel now selected for CyTOF files.
    • Removed presets functionality.
    • PDFs were not creating attachments.
    • Non-FCS files were not being added as attachments.
    • Attachments were not being cloned.
    • If the user collapsed the SPADE analysis setup content box (center pane) or the analysis controls content box (sidebar), they are now opened for a new analysis.
    • There is now a button to go back to a SPADE analysis if you click on the static Population view from the SPADE analysis page.
    • The name of the saved SPADE analysis now shows up on the SPADE analysis page.
    • Merged nodes on SPADE analyses were jumping to upper left corner when samples were changed.
    • SPADE global coloring range was not using percentile clipping.
    • SPADE bubble labels stay put after a reload.
    • Import gates for tailored gates was misdefining populations.
    • Fixed reset visualization on SPADE analysis page.
    • SPADE analyses now show up on experiments that are viewed via projects.
    • SPADE now works on Windows 7/Chrome.
    • When a bubble was selected on a SPADE analysis, no other node information was showing up on the node attribute table.
    • Changing samples on SPADE analysis was resetting column selections on node attribute table to all channels.
    • 2-d plots on SPADE analysis page were not updating when samples were changed.
    • Cloning an experiment was obliterating the selection in FCS files dimension on the saved illustrations.
    • Selected bubbles were not showing up in the export box on SPADE analysis page.
    • SPADE copy analysis settings is fixed.
    • A user with public-only access to an experiment cannot create a SPADE analysis.
    • Global color setting on SPADE analysis now works when you change samples (was setting all nodes to black).
    • Existing SPADE analyses are now visible to users with public-only access to an experiment.
    • A heatmap with an empty square now works (was throwing an exception).
    • Changes to a SPADE analysis now register as a change to the whole experiment, updating the “Last updated” value.
    • Links in the “Did You Know?” frame now open in new tabs.
    • A user with project access to an experiment, where the project is set to view-only, no longer has access to the “reset working illustration” button.
    • Can no longer remove all the columns from the SPADE node attribute table.
    • The fold change baseline selected was not being saved for SPADE analysis setup.
    • Could not uncheck baselines on the SPADE analysis fold change setup page.
    • Inbox filters were temporarily broken.
    • Someone who uploads an experiment who has no other access to the experiment no longer sees it on the inbox.

    Release Notes for Cytobank v2.5.6

    Published on May 25, 2012

    You may have noticed a few additional tweaks to PDFs pop up in the form of 2-5-5-1, -2, -3, and -4 releases over the past few weeks. Well, now that those adjustments have been made, we’ve rolled out our latest release of 2-5-6, including expanded FCS file support and admin tools. Read on to learn more about these as well as some bug fixes.

    New Functionality

    • FCS 3.1 files are now supported.
    • Administrators can now navigate back to the user database instead of having to return back to the Inbox.

    Bug Fixes

    • FCS files with no events are now supported.
    • An error message now appears (instead of an exception) if you import a compensation matrix without selecting a file or experiment from which to import.
    • The link to the primary researcher (PR) on the admin page under the “Newest Experiments” heading now leads to the profile page for that user, instead of the edit page for that user’s profile.
    • Autocompensation now shows a standard dot plot, regardless of the plot type selected on the working illustration.
    • Creating an experiment from gated files, cloning files from an illustration, selectively cloning an experiment, cloning an experiment, and cloning FCS files now all use one credit.
    • All Getting Started links now point to our new documentation site.

    Release Notes for Cytobank v2.5.5

    Published on April 29, 2012

    New Functionality

    • In the Export Events box on the Working Illustration page, the name “Compensation” was changed to “Exported Compensation” to clear up possible confusion.
    • The session timeout is set to 8 hours (increased from 3 hours) and a warning has been added to the green Getting Started box in the gating applet.
    • There is a new filter in the Inbox called “My experiments and shared,” which displays your experiments plus ones shared with you (as per user request).
    • If an Illustration is longer than 200 inches, an information message tells the user to open the resulting PDF with an alternate program such as Preview (for Macs) or with Adobe Illustrator (Mac or PC), as Adobe Reader cannot display a PDF exceeding these dimensions.

    Bug Fixes

    • Fixed errors with PDF display of exceptionally large plot sizes (256 px and 512 px), though we are still working out some kinks.
    • A PDF of an Illustration with the populations dimension not selected no longer creates an error.
    • An FCS file with no events no longer causes an error on the Illustration.
    • 256px and 512px plots fit better on letter-size PDFs.
    • When an Illustration fits on a letter-size PDF, plots are no longer truncated at the page break or on the right-hand side.
    • When an Illustration is too wide for a letter-size PDF (or other sizes), and error message appears advising the user to select a different size.
    • “Overlaid” dimension labels on histogram overlays on PDFs no longer look crowded.
    • Importing tailored gates now changes the “updated” timestamp for the experiment.
    • If the Channels dimension is not active, the print view will display an error message.
    • If you try to open the gating applet in Windows 7/Internet Explorer 9, it doesn’t work. A warning now shows up in the green Getting Started panel explaining that it’s a known issue.
    • A gate with no events no longer causes an error on the Illustration with heatmaps.
    • Emails to new users now include a link to the new support site.

    Release Notes for Cytobank v2.5.4

    Published on March 7, 2012

    New Functionality

    • Users can now select size formats for their PDFs, including several fixed sizes (Letter, A4, and Poster) and two auto-fit sizes (Large and Infinite). This also resolves an issue where a lot of extra blank space was found at the end of PDFs. We’ll be publishing a blog post soon explaining all our recent PDF enhancements, so stay tuned.
    • The FCS file list on the experiment summary page now loads independently from the rest of the page.
    • Tailored gates can now be imported from an existing experiment.
    • PDFs now display plots sized according to the specifications in the Working Illustration (64 px, 128 px, etc).
    • Added a download progress bar to the Stanford FACS Facility import page.
    • Added a session time-out reminder in the gating applet, informing people of the need to Save and Return if they plan to walk away from analysis for more than 8 hours.

    Bug Fixes

    • Fixed an issue with improper functioning of the name search fields (for setting PI/PR, sharing with someone, etc).
    • The support page, which has been redesigned, now opens in a new browser tab.
    • PDFs for saved illustrations no longer have a date/time stamp for the ‘Updated’ value in the header, since saved illustrations cannot be updated. Working illustrations still have that date/time stamp on the PDF.
    • Blog links all open in a single tab, instead of spawning multiple tabs.
    • For Stanford users, retrieving an experiment via a URL now uses one credit. (Credits may be increased any time.).
    • Compensation files are no longer shown as options for the “Percent in Gates” selected gate drop-down.
    • When an experiment is cloned, its associated labels are no longer cloned.
    • X axis labels had disappeared from plots shown on the upload success page; they are restored.
    • An issue was occurring where a gate was set to tailored gate status, check gates was clicked, and then additional gates were tailored, and a subsequent “Check Gates” did not reflect the newer gate positions. This is now fixed.
    • Fixed an issue where users were not warned when they had “Use Channel/Panel Values” selected but did not have the Channels figure dimension enabled. This was previously causing an error.
    • Resolved an issue resulting in truncation of plots horizontally in PDFs when long row labels were present.

    Release Notes for Cytobank v2.5.3.4

    Published on February 13, 2012

    We just released a fix for the Yahoo OpenID login button, which was briefly not working following an update by Yahoo.

    Release Notes for Cytobank v2.5.3.3

    Published on February 7, 2012

    Today we released an update that fixes a bug that was causing some users to be unable to select their name as PI, PR, or in the sharing box.

    Release Notes for Cytobank v2.5.3.2

    Published on January 21, 2012

    We released a quick update that directs users to our newly redesigned Support page when they click the “Support” link at the top of the Cytobank page.

    Release Notes for Cytobank v2.5.3

    Published on January 11, 2012

    New Functionality

    • A user’s PI (designated by the user) is now given full access to the user’s experiments by default. Access can be removed by unchecking the checkbox when creating the experiment or by removing the user on the experiment summary page.
    • The ability to assign kits to experiments has been removed.
    • If there are channel conflicts, a warning message is displayed on the main illustration page.
    • The clearer description of permissions levels is provided when setting up projects.
    • The import file compensation page has clearer instructions.

    Bug Fixes

    • Long column names now wrap properly in PDFs.
    • Improved the performance of opening illustrations for experiments with many tailored gates.
    • Improved the performance of running the “Check gates” functionality when using tailored gates on a large number of files.
    • Fixed a bug with quad, split, and range gates.
    • Exports made with the “FCS Files” dimension active no longer have “.fcs” in the middle of the filename.
    • The “Top Channels” Inbox filter is working again.
    • Colors can now be selected for contour and shaded contour plots.
    • Attachments now properly show who uploaded them (previously, they showed the experiment owner as the uploader).

    Release Notes for Cytobank v2.5.2

    Published on November 30, 2011

    New Functionality

    • There is a status page for Cytobank employees to help us monitor performance and look for places to improve performance.
    • The default scaling parameters for CyTOF data files have been changed, as CyTOF software now spreads the data around zero. The new default parameters are the following: Scale = Arcsinh, Cofactor = 5, Min = -5, Max = 12,000.
    • Graphics tweak: the shadow for tooltip popups is now black instead of gray; this will make the look of plots behind the tooltip a little cleaner.
    • If a user selects only one channel when creating a compensation matrix, an error message now appears asking the user to select at least two channels, and channel options are presented again.
    • Reworded “Request more credits” to “Get more credits” to reflect the fact that credits are always immediately available upon request.

    Bug Fixes

    • Labels for the “overlaid” dimension on histogram overlays now appear on PDFs; they were missing from the new PDFs.
    • QR code has been fixed on the new PDFs for a minor URL problem.
    • Fixed a bug where clicking on a label to filter the inbox wasn’t working.
    • The sample name listed for the gating hierarchy on the new PDFs is now in original sample case instead of all caps.
    • Fixed a bug where labels for public experiments were not properly displayed on the experiment summary page.
    • If no populations are selected, you now get an error message when you try to export events reminding you to select a population.

    Release Notes for Cytobank v2.5.1

    Published on November 10, 2011

    The latest release of Cytobank is live on our servers, including some new functionality and a few bug fixes. Of note this time around, we’ve altered the way Inbox filters work. You can now filter the list of experiments you see in your Inbox by choosing to view only experiments you uploaded or those for which you are the primary researcher (“My Experiments”), experiments that others have shared with you directly or through projects of which you are a member (“Shared with me”), experiments that have been made public to everyone on Cytobank or your hosted server (“Public experiments”), experiments you have archived (“Archived experiments”), or experiments you have deleted (“Trash”). You can read more about the new experiment filters on our documentation site. Stay tuned for an upcoming post highlighting functionality that will help you keep your inbox organized!

    New Functionality

    • The “Active experiments” inbox filter was renamed to “My experiments,” and now only displays experiments you uploaded or experiments for which you are the PR.
    • The “Plate” figure dimension now pulls information from the PLATE_NAME attribute within FCS files, with PLATE_ID used in its absence.
    • Added additional instructions to the auto-compensation wizard pages.
    • Added message notifying users when there are no experiment files present when a user attempts to display a gating hierarchy for all files (this feature will not work if only compensation files are present).

    Bug Fixes

    • The “Shared with me” filter now only shows experiments that were shared with you, either directly or via projects of which you are a member. We fixed a bug where experiments for which you were PR were showing up in this list if the experiments you owned were part of a project created by someone else that was shared with you (whew).
    • Scale settings are now transferred when creating an experiment from gated files.
    • Channel names for duplicated files now mirror that of the parent file when using the Duplicate Files feature on the annotation pages.
    • Fixed a bug where a manager could not be added to a project.

    Release Notes for Cytobank v2.4.5.1 – v2.5.0.1

    Published on November 4, 2011

    In the latest releases to Cytobank, we have made some big improvements to PDFs of your saved illustrations. The biggest change you will notice is that the data contained in PDFs are now displayed on one continuous, scalable page. This makes it easier for you to excerpt your data when preparing figures, and fixes a previous issue with especially wide or long plot sets getting truncated. Stay tuned for a blog post that will put these changes in context.

    New Functionality

    • PDFs now display all of the content on one scalable page.
    • You can now specify a name for PDFs prior to download.
    • The Gating Hierarchy display now mirrors that seen in the Working Illustration, using space more efficiently.
    • PDFs have a new look, with a cleaned-up header.
    • Added text instructing user how to figure out where the PDF was saved on their computer.
    • Added notification that PDF generation has completed.
    • When you download a PDF, it is automatically added to the experiment as an attachment, listed under Attachments on the Experiment Details page.

    Bug Fixes

    • Fixed an issue where gates and populations were migrating over to the new experiment when using Create Experiment from Gated Files.

    Release Notes for Cytobank v2.4.4 – v2.4.5

    Published on September 20, 2011

    Of note, we have added a “selective cloning” feature that allows you to create a new experiment that contains a subset of an existing experiment’s FCS files. This would be a handy way to split files off into a new experiment if a subset of files use a different compensation matrix, or to separate debarcoded files generated with our “Create Experiment from Gated Files” feature (stay tuned for a post on Fluorescence Cell Barcoding).

    New Features

    • Selective cloning is now available. This allows a user to clone an experiment with a selection of FCS files (instead of all the files). Clone FCS files and Clone experiment (where all FCS files are used) are still available.
    • There is a new “Profile” link at the top of the page to make it easier to get to your profile. Among the things you can do on your Profile page, you can change your email address, change your PI, and change the default contents of your Inbox when you first land on that page (e.g., to see only your experiments, or always see “All Experiments”). The “Welcome, Username” link will also bring you to your Profile page.
    • A user’s PI is now the default PI on selective clones. All full access users are listed as options for PI. There is a checkbox to make it easy to give full access to the PI, similar to the one in place for creating new experiments.
    • All attachments can now be downloaded in a single zip file.

    Bug Fixes

    • Fixed a bug where quad/split/range gates were not being drawn properly.
    • When we updated projects so that managers have full access to all experiments regardless of the settings for members/leaders, there was a bug where existing managers already on a project were not getting access to the new experiments. Managers who were already on a project will have full access to experiments added to the project from now on. This is not retroactive for experiments that were on the projects before the last release.
    • A bug was fixed that made “Percent in gate” unavailable as a plot statistic if “Ungated” was selected; now it’s only unavailable if no gates have been drawn.
    • The gating applet now handles large numbers of tailored gates without crashing.
    • When gates are deleted, the status is saved in the gating applet (even without clicking “Save & Return”). This fixes a bug where deleting a gate and then importing gates led to the deleted gate sticking around.

    Release Notes for Cytobank v2.4.3

    Published on August 8, 2011

    We recently rolled out our latest release to the servers. A couple changes we’d like to highlight. First, managers of projects now have full access to all experiments in those projects. (Read more about projects on our documentation site.) We’ll have a separate blog post discussing projects [updated 08/22/2011] and how you can use them to share groups of experiments with colleagues. Second, you can now archive experiments in your Inbox. This is a new feature that has been frequently requested, and we’re excited to finally roll it out to you to help you better organize your experiments!

    New Features

    • Managers of projects now have full access to all experiments in those projects (regardless of the level of access set for project members). This is not retroactive for existing projects. Read more on our documentation site.
    • You can now archive experiments in your Inbox. Archived experiments will be designated with an “A”. You will not see archived experiments unless you are viewing “All experiments” or “Archived experiments”.Read more about Inbox filters on our documentation site.
    • We now handle FCS files exported from FlowJo that have blank reagent (long channel) names. This can result if you have not annotated the reagent (e.g. CD3 PE-A) in FlowJo. The field now defaults to the short channel name (e.g. PE-A).
    • Creating an experiment from gated files (an option on the Working Illustration page) now works like a full experiment clone – all illustrations, annotations, and compensation files are included in the new experiment.
    • Filenames ending in a letter and two numbers (e.g. filenameA01.fcs) are now recognized as plates. This is the default for files exported from CellQuest.

    Bug Fixes

    • Fixed an issue where a user’s PI/Manager could not be entered or updated on a user’s profile.
    • Fixed an issue where kit-templated gates did not show up until you entered the gating applet.
    • Clicking reset on an annotations page (such as Conditions or Timepoints) now prompts you to make sure you want to reset and remove all tags.

    Release Notes for Cytobank v2.4.1.3 – v2.4.2

    Published on July 23, 2011

    New Features

    • Performance updates were made to speed up processing, particularly in experiments with a large number of compensated channels.
    • You can now duplicate an FCS file in an experiment (instead of having to upload an additional copy of the file). This is useful in cases such as the following: 1) you want to assign a file to multiple conditions or doses or 2) you collect one unstained file but want to show it in an overlay for multiple staining panels.
    • Tube name or sample name are now visible in addition to the filename in the drop-down menu in the gating applet. (Note that if the filename is too long, the tube or sample name may be either truncated or not displayed.).
    • The experiment summary page now provides an estimate of an Illustration’s size and content by listing the Figure Dimensions used in the Illustration. Example: Channels (4) x Conditions (7) x Populations (1).

    Bug Fixes

    • If required information is not provided when creating an experiment, an error message is now generated.
    • Fixed an issue with tailored gates being duplicated when copies of an existing file were added to the experiment.
    • The percentile algorithm has been updated.
    • Fixed an issue with the availability of the percent in gate statistic. The statistic is now available except in these instances:
      • When “Ungated” is selected, with or without other gates.
      • When no gates are selected.
    • Fixed an issue with timestamps on Illustrations and experiments:
      • Saved illustrations now only display a “Created” timestamp.
      • The “Updated” timestamp for your Working Illustration is now updated when you click the “Update Illustration” button.
    • Fixed an issue with experiments created from cloned files where a default channel was not selected (and thus a default illustration could not be displayed).
    • Fixed an issue where Cytobank did not recognize “SS Log” as a side scatter channel.
    • Renaming a tailored gate now renames the gate on all files.
    • When importing compensation, gates, or annotations (such as conditions) from another experiment, the drop-down menu no longer lists the current experiment as the default.
    • We have removed the Presets menu on the Working Illustration page (which set up Illustrations for specific pre-set conditions).

    Release Notes for Cytobank v2.4.0.1 – v2.4.1.2

    Published on June 16, 2011

    We’ve released a considerable number of changes to Cytobank over the past six weeks. Many of these new features are not yet visible to our users, because they operate in the background to power Cytobank Reports. You can see Cytobank Reports in action by viewing the Report created for the Nolan Lab’s recent mass cytometry study. Cytobank Reports also powers the datasheets in the BD FACSelect Buffer Compatibility Resource. In the near future, users will be able to use these features and create their own Reports to showcase their data and analyses. What is visible for our users is an updated interface for Figure Dimensions. We’re excited to introduce these changes, as we think they make selecting your files and rearranging plots even easier than before. We’ll be discussing these changes in more detail in a future blog post. [Updated 07/22/2011]

    New Features

    • Functionality for Cytobank Reports has been added.
    • The Figure Dimensions interface has been updated.
    • The “Edit” link on most Figure Dimensions is now called “Setup”.
    • A new link called “Choose” opens a lightbox (a pop-up window displaying the Dimension tags) where you can more easily select which tags you want to show in your Working Illustration.
    • You can now modify the layout of your plots by re-ordering the tags in the lightbox – drag them up and down using the gray “grab” handles. You can still re-order Dimension elements in the Layout Placeholders tab in your Working Illustration.
    • You now have the option of selecting one or more cell types as “Source(s)” in your Experiment Details. You can also leave it blank.
    • The list of files in the gating applet now displays more files per “page” in the drop-down menu.

    Bug Fixes

    • Improvements have been made to entering and exiting the gating applet.
    • The compensation matrix in your Working Illustration is now set to what was last used in the gating applet.
    • Import Gates (in the gating applet) now defaults to a blank selection, prompts for a confirmation to import gates from the selected experiment, and displays a success message.

    Release Notes for Cytobank v2.3.4.1

    Published on April 29, 2011

    This update contains an important fix for those of you who have upgraded to Firefox 4, as well as layout changes to most of the Annotation pages. The update this week fixes an issue with the gating applet that was preventing it from loading properly in Firefox 4. There are a few remaining issues that we are aware of. On a Mac, pop-up windows like “Manage Populations” do not seem to be working properly. Click on the Java icon that appears in the dock to see the pop-ups. If you get a Java icon in the gating applet area, try reloading your browser. As always, please submit a support ticket if you notice other issues.

    Most of the Annotation pages have been updated for ease of use. The “Add” text box (in which you can type a comma-separated list of tags) has been moved to the main section of the page. These pages also now contain links to hop directly to the Timepoints, Dosages, Conditions, Individuals, or Sample Types pages. For example, after tagging your files with Timepoints variables, you can now click “Edit Conditions” under “Actions” on the left sidebar to be taken directly to the Conditions page, without having to return to your Working Illustration.

    New Features

    • The “Add” text box on most Annotation pages has been moved to the main section of the page.
    • Links have been added to most Annotation pages to make it easy to hop to and between the Timepoints, Dosages, Conditions, Individuals, and Sample Types pages, without needing to return to the Working Illustration. Annotations are automatically saved as soon as you leave the Annotation page.
    • “Getting Started” boxes have been added to most Annotation pages.

    Bug Fixes

    • The gating applet now loads properly in Firefox 4.
    • Fixed an issue where turning a tailored gate back into a global gate deleted the associated population.

    Release Notes for Cytobank v2.3.4

    Published on April 8, 2011

    The most visible change to all users may be the new Getting Started boxes (more after the jump). Another change will be noticeable to those using Cytobank on their iPhone or iPad (see our recent blog post about Cytobank on the iPad).

    The Getting Started boxes are the green boxes at the top of the Inbox, Experiment Details, Working Illustration, and Compensation pages, as well as at the top of the Gating Applet. (You may need to click on the arrowhead in the green title bar to expand these if you’ve previously minimized them.) We’ve updated the text and links in these boxes. The linked video tutorials open directly in a lightbox on the page so that you can view the video without losing your place in Cytobank. We hope these new Getting Started boxes will provide useful tips and guidance.

    New Features

    • Gates are now drawn at one-pixel thickness regardless of plot size, for easier viewing.
    • Export options for FCS files and gated events are now better organized on the Working Illustration page.
    • You can now see the scale settings for someone else’s experiment if you have illustration access.
    • The custom compensation matrix table now has more descriptive labels for the rows and columns.
    • We’ve clarified that plot scales can be edited on your own experiment.
    • Functionality on iOS devices (iPhone and iPad) is now improved for dragging and dropping (for example, rearranging Figure Dimension boxes).
    • A link to our blog has been added to the top of the Cytobank application.
    • “Delete My Saved Illustrations” now provides a warning popup to fend off accidental clicks.
    • Emails that notify users about experiments that have been shared with them now reply to the experimenter’s email address (instead of a generic Cytobank support address).
    • Pairwise plots (accessible from “Advanced Views” on the Working Illustration) now have tooltips, popups that appear when you hover over the plot that provide the X and Y axis labels, to help identify plots in matrices that are very large.
    • Getting Started boxes have been updated with new text and tutorial videos that open up in a lightbox on the current page.

    Release Notes for Cytobank v2.3.2 – v2.3.3

    Published on March 21, 2011

    One change that may not be immediately apparent to existing Cytobank users is that we now send an email verification link to new users when they first register. We also send a verification link if existing users update their email addresses. Users will still be able to access Cytobank if they haven’t yet verified their (new) email address.

    Need to update your registered email address? Click “Profile” at the top of the Cytobank application and then click “Edit” in the left sidebar.

    New Features

    • Functionality for pairwise plots is now available under “Advanced Views”.
    • A new “Delete My Saved Illustrations” button on the Experiment Details page enables users to delete all of their saved illustrations for that experiment.
    • “Help” link has been renamed “Support”.
    • Tube name is now extracted from DiVa files in various places such as compensation pull-down menus.
    • The success page for file upload now includes file size units.
    • New statistic has been added: Pearson R (X vs Y), which reports the correlation coefficient for the x-axis vs the y-axis (note that this is not available for histograms, heatmaps, or heat plots).
    • Top Channels now loads only when requested, enabling the Inbox to load more quickly.
    • The option to export a table of scaled events is now available.
    • We now verify email addresses when users first register and if/when they update their email addresses.
    • Scales for Accuri experiments are now set automatically (similar to CyTOF) .

    Bug Fixes

    • Experiments can now be permanently deleted from Trash.
    • Fixed an issue where plot statistics could not be turned off for heatmaps and heat plots.
    • Fixed an issue where exported Table of Events only contained the first row of values repeated if compensation was enabled.
    • Fixed a rare issue where the cache reads a file incorrectly.
    • Fixed an issue where some support tickets were not being sent correctly.
    • Fixed an issue where cloning an experiment doubled plate-related tags.

    Release Notes for Cytobank v2.3 – v2.3.1.2

    Published on February 8, 2011.

    New Features

    • New statistic has been added: Percentile Distance (5 to 95).
    • The total file size for an experiment is now shown on the success page after experiment files are uploaded.
    • Files now filter on the tube name in an annotation dimension (e.g. conditions), when before they only filtered on the file name.

    Bug Fixes

    • Sharing illustrations no longer creates extraneous illustrations for the original user.
    • Plot tables now show up only at the bottom of each illustration (instead of between each row).
    • Empty experiments that are part of a project no longer show up until files are added.
    • Experiments without FCS files can now be deleted from the upload files applet.
    • Plot statistics can now be turned off for histogram overlays.
    • Cloning an experiment now maintains the categorization of files (experiment, compensation, other).
    • We love getting feedback from our users! You can send us comments or questions by email, tweet, or by submitting a ticket through our support portal.

    Release Notes for Cytobank v2.2.9 – v2.2.9.1

    Published on January 12, 2011

    Bug Fixes

    • Fixed an issue with cloning where cloning a full experiment did not clone reagent names.
    • Fixed an issue with cloning where cloning a full experiment did not clone the compensations for illustrations.
    • Fixed an issue where empty spaces in the plot layout prevented heatmaps and histogram overlays from rendering.
    • Fixed an issue with percent in gate statistic not working properly with tailored gates.
    • Fixed an issue that occurred while tagging an experiment that had just been reset.
    • Fixed an issue with gates where gates were still drawn when “Show Gates” was turned off and “Show Gate Statistic” was turned on.
    • Fixed an issue where uploading more files to an existing experiment would cause the progress bar to freeze during preprocessing of the data.
    • Fixed a redirect that caused an incorrect page to load after recategorizing files on the experiment upload page.
    • Channels are now automatically selected in an illustration after a full clone.
    • If a custom compensation matrix is deleted, all illustrations using that compensation matrix will have their compensation setting reverted to File Internal.
    • “Reset Experiment” now has a confirmation message.
    • As always, we welcome any feedback you might have. You can get in touch with us by email, Twitter, or by submitting a ticket through our support portal.

    Release Notes for Cytobank v2.2.6 – v2.2.7.2

    Published on December 20, 2010

    New Features

    • Created an initial version of an automatic compensation wizard.
    • Added an option to display number of events in a gate instead of percentage of events.
    • Added the ability to use tailored gates on histogram plots.
    • Added the ability to import gates and compensations from public experiments.

    Performance

    • Database optimizations to speed load times for the experiment details page.
    • Javascript optimizations to reduce unnecessary work when making updates to an Illustration.
    • Backend optimizations to improve memory management

    Bug Fixes

    • Fixed an issue with receiving double success messages when an experiment is created.
    • Fixed an issue with experiment variable tags so that searching for tags is no longer case-sensitive.
    • Updated wording in welcome email to new users.
    • Added a better success message for “Reset Illustration” function.
    • Fixed an issue with auto-channel selection in CyTOF files that contain parentheses in the channel names.
    • Fixed an issue with projects with the same name created by different users.
    • Fixed an issue with “Reset Experiment” such that the action now properly deletes all compensations in that experiment.

    Release Notes for Cytobank v2.2.5

    Published on October 22, 2010

    We’ve fixed some caching/performance related bugs. Now, after you’ve opened an illustration for the first time, subsequent reloads should happen much more quickly. This should be very apparent when you start rearranging your dimensions. The second new feature of note is the ability to see the Percent in Gate of a selected gate’s events when compared to the selected/active populations in the figure dimension. This statistic was displayed only on the plots previously, but it can now be shown in the table of statistics below each plot group for easy cutting and pasting to other software.

    New Features

    • Add statistic to illustration: percentage of events in Selected Gate (when compared to parent/active population).
    • Added a new filter option to the Inbox: “My uploaded experiments”.
    • Updated the options for Default Inbox Experiments Filter in the user profile to allow a choice of any available filter as the default.
    • Added optional Location, Company/Organization, and “How did you find out about Cytobank?” fields to the registration form.

    Bug Fixes

    • Display issue in the Gating Hierarchy.
    • Failure when trying to export VERY large experiments.
    • Fix for gating applet plot choice behavior when using histogram overlays or heatmaps in the illustration.
    • Fix for range gates not displaying on histograms in the illustration view.
    • Fix for PDF generation not working when FCS files contain quotes in the filename.
    • Fix to make sure all compensation matrices are copied over when exporting gated data to a new experiment.
    • Fix for an error caused when an upload attachment is clicked with no file selected.
    • Fix for an error in the Top Channels list when a user has no experiments.
    • Fix for a performance issue that caused unnecessary calculations to happen when building an illustration.

    Release Notes for Cytobank v2.2.4

    Published on October 5, 2010

    New Features

    • Added the display of a table of statistics for all plot types and enabled related statistics controls.
    • Added “log base 2″ equation to the Plot Statistics: Equation menu.
    • Added “Transformed Median” and “Arcsinh Median” options to the Plot Statistics: Statistic menu.
    • Added a field so that users select “Percentile” and type in a value from 1-99 now instead of just having “95th Percentile” as the only option.
    • Added “Heat Plots” (pseudo-3D mountain plots) to the Plot Type.
    • Added Z-axis plot control for use in Heat Plot Mode.
    • Added “reset working illustration” button to the Experiment Summary page so the user doesn’t have to load their Working Illustration in order to reset it.
    • Added a button to create a new experiment from gated FCS files, useful for de-barcoding experiments.
    • Improved IE8 support.
    • Added the ability to view the gating hierarchy for all files at once (as opposed to one file at a time).
    • Added a setting to default the Inbox view to “My Experiments”.

    Bug Fixes

    • Fixes to histogram overlay compensations.
    • Fixed caching bugs.
    • Fixed issue with dragging labels in layout placeholders.
    • Fixes to PDF support.
    • Fixed caching of illustration page tabs.
    • Fixes to prevent compensations being locked in.
    • Fixes to make sure uploaded compensations are available in the gating applet.
    • Fixed a bug with negative event counts for files with extremely large numbers of events.
    • Fixes related to gate and population deletion.
    • Fix to make sure illustration images are correctly updated when plot scales are changed.
    • Fix to “Check Gates” in the gating applet. It was displaying incorrect populations in some cases.
    • Fixes to scales when adding new files to an existing experiment that contains FCS Files from the CyTOF mass cytometer.
    • “Save Illustration” now redirects back to the Experiment Summary page on success, preventing extra illustration reload, helpful for very large illustrations.
    • Optimizations to speed up the loading of the annotations pages (Conditions, Timepoints, etc.).
    • Optimizations to speed up the loading of the experiment summary page.
    • Updated instructions for how import a Flowjo compensation file.
    • Lots back-end memory/performance optimizations (still very much ongoing!).

    Release Notes for Cytobank v2.1.4

    Published on April 23, 2010

    • Added a post-logout page to provide users with a link to logout from their OpenID provider.
    • Added the ability to add experiments to a project from the “edit project” page.
    • Added the Top Channels and Experiment Variables filters to the left menu of the Inbox page.
    • Added support for importing FlowJo compensation files.
    • Added Log2 Ratio as another comparison equation for heatmap and histogram overlay illustrations.
    • Updated the Plate Dimension in the illustration to be populated with the value from keyword PLATE NAME instead of PLATE ID.
    • Updates to make detection of data files from CyTOF machines more accurate.
    • Bug fixes related to both importing/exporting compensations and creating compensations in Cytobank.

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