What's New?

2026-04-13

Persistent SDK Versions after IDE Restart

You no longer need to reapply your SDK version after rebooting an IDE. When you update the SDK with update_sdk_version() (Python) | updateSDKVersion() (R), the SDK version you select persists automatically. This update eliminates extra setup steps and helps you stay current without interrupting your workflow.

NOTE
SDK version retention applies only to IDEs created after April 14. For IDEs created before that date, run update_sdk_version() (Python) or updateSDKVersion() (R) once to activate the retention capability. For details, see Update the SDK Version (Tutorial) .

R-Based Support of Pixi Packages in GitHub

You can now use the installGithubPackageToPixiEnv() SDK to install R packages from GitHub into an existing Pixi IDE environment. This gives you more control over the R tools in your IDE. You can add project‑ or lab‑specific packages whenever you need them. You can also try R package versions that aren’t part of your standard Pixi setup. This precludes the need to file a ticket or wait for someone else to update your environment when you want to try a new package. For details, see Install an R Package from GitHub into a Pixi Environment .

Enhanced Support for Multiple Conda and Pixi Upload Environments
When you upload files from an IDE that's using a different Conda or Pixi environment than the one it was created with, HISE now detects the mismatch and prompts you to choose which environment to associate with your files. This keeps your uploads tied to the correct environment without any extra setup or workarounds. For details, see Save a Custom Conda Environment (Tutorial) , Save a Custom Pixi Environment (Tutorial) , and Install a GitHub Package in a Pixi Environment (Tutorial) .

2026-04-09

Info/Warning/Alert Banners Announce Important HISE Updates

You’ll now see a banner in HISE when there’s something important you should know, like a maintenance notification, resource stockout, or key feature update. These messages can appear on specific pages or across HISE. They’re dismissible, so you get timely, relevant information without unnecessary clutter or distraction.

2026-04-01

Data Discoverability for Pubic Releases

HISE has data discoverability features that let you explicitly choose which fields to include in the public data that becomes findable in Advanced Search. Human metadata (lab results, EMR data, and survey responses) is now excluded by default. To make public data releases discoverable, you must review the listed fields and opt in to those you wish to include.

In other words, you opt in selected data instead of opting out. This new data discoverability process keeps sensitive data hidden unless you explicitly choose to reveal it, helping you avoid accidental exposure of confidential data. But the process also makes it easy to share key data where necessary for transparency and reproducibility.

Makes chosen fields searchable in the PUBLIC FILES tab of HISE Advanced Search. When you turn on a field in data discoverability, it becomes part of that release’s public metadata. This metadata appears as a filter option in Advanced Search under the PUBLIC FILES tab. HISE users can then filter for that field (for example, a specific lab result or survey answer) to find your public data.

Supports compliance. Because sensitive fields must be explicitly selected to become publicly discoverable, the new discoverability process safeguards patients' data and complies with legal and ethical standards for handling confidential data.

Uses the same workflow for publications and Data Apps. You configure data discoverability in the Collaboration Space, where your HISE publications and Data Apps are housed. Handling your Certificate of Reproducibility is just as straightforward. New tools let you easily confirm that you've reviewed the appropriate human metadata fields and you're ready to release the selected data (if any) publicly. For details, see Manage Data Discoverability (Tutorial) .

2026-04-01
Exported Billing Offers Greater Detail about Scientific Program Spending

Exported CSV files for scientific program billing (currently available to admin users only) now include columns for Account Name, Billing Project Name, IDE Name, and IDE Cost. You can easily drill down on each account to track current spending and predict future resource needs.

2026-03-11

HISE Now Supports Pixi

HISE now supports Pixi to build and manage IDE environments. Behind the scenes, Pixi uses the same package sources as Conda, but it builds IDEs faster and more reliably. That means uploads are faster, and the environment fails less often. For details, see Use the Pixi Environment.

• Faster upload_files in Pixi IDEs. In regular mode (that is, non–fast mode), upload_files is significantly faster in Pixi IDEs than in comparable Conda IDEs. For example, a minimal Conda environment takes 15–20 minutes, while the same workflow in a minimal Pixi environment takes 6–10 minutes.

• Flexible content migration from Conda to Pixi. If your current IDE uses Conda, you can create a Pixi environment that reflects your existing setup and then launch a new IDE with that Pixi environment. Your Conda IDE stays as is, and you choose when and how to move your work into the Pixi IDE (for example, by opening the same project repo there or by copying specific notebooks). For details, see Convert a Conda IDE to a Pixi Environment (Tutorial).

• Single dashboard for Conda and Pixi. You can use Pixi without affecting your current configuration. On the Manage Environment Packages page in HISE, you can toggle between Conda and Pixi. Choose Pixi, and then select a saved Pixi environment, or follow the regular IDE workflow (Research > IDEs) and save a Pixi environment from scratch. Of course, Conda environments are still available as well.

• Reusable package setup. When you use the Python SDK to install a GitHub package into your Pixi environment, the SDK records the build details and makes that package available each time you create a new IDE from that environment.

2026-03-04

Download Files to Your Laptop

You can now securely download certain HISE files from Advanced Search to your laptop for use in tools like FlowJo or Xenium Ranger. Look for files marked Downloadable, and then use the download icon to save the file to your usual download location.

2026-02-25

Ask Avery Chatbot Is Your HISE Assistant

The Ask Avery chatbot is now available throughout HISE to help you find answers about the platform without leaving your current page. Ask Avery returns fast, conversational responses to your questions about HISE IDEs, features, and workflows by searching across our documentation set. To get started, click the speech bubble in the lower-right corner of your screen in HISE, click Request Access to authenticate with Google, and simply type your question. Use the built-in feedback options or contact Support to let us know how well Avery answered, so we can continue to improve the experience.

2026-02-04

Xenium Pipeline Automates Tissue Identification within Blocks That Contain Multiple Tissue Specimens

The Xenium pipeline was updated to support the tissue block where a single slide contains multiple tissue specimens. Only correctly labeled tissues advance downstream. This additional validation step helps you avoid spending time and other resources analyzing misidentified samples, giving you greater confidence in every result.

2026-01-21

Advanced Search Redesign

We've redesigned the HISE Advanced Search feature with an intuitive, filter-based interface. Instead of writing database queries, you start with a broad category (files, samples, or subjects) and then use filters to narrow your results. These dynamic filters are organized into logical groups, such as File Metadata, Sample Metadata, Subject Metadata, Lab Results, Surveys, and Custom Metadata.

First, choose one of the three basic search types described in the following table.

Then add relevant filters. As you apply each additional filter, more granular, context-specific options appear. Each filter uses operators, like equals or contains term, paired with your chosen values. In the results window, after you select the results you want to keep, a floating options menu helps you move the results downstream:

• Add files to an existing file set

• Create a new file set

• Send results to an IDE for analysis

• Visualize results for specified file types

In the new Advanced Search, saved queries are regarded as research assets that document how your cohort or data set was defined. Sharing queries is as easy as copying a URL. You can make a query available to specified collaborators or to all account users. Queries are now unsaved and private by default, and adjusting their visibility doesn't affect underlying project data permissions.

For details, see the Release Notes. If you have questions about using Advanced Search, contact Support or see the following docs:

• Understand Advanced Search Concepts

• Use Advanced Search for Basic Queries (Tutorial)

• Use Advanced Filters for Complex Search Queries (Tutorial