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The Slides Viewer lets you inspect supported microscopy and whole-slide images inside your Purna workspace. Open a slide alongside your conversation, zoom into tissue, and save regions with names and notes without changing the original image.
Purna Slides Viewer for inspecting microscopy images and selecting regions of interest

Inspect a slide and keep regions of interest alongside your workspace.

Opening a slide does not identify cells, segment tissue, calculate statistics, or perform a biological analysis. The controls available depend on the information already present in your file.

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Supported files

The slide size limit is 500 MiB per file. A successful upload does not guarantee that every image layout or encoding can be viewed. Extensions are case-insensitive; keep the full filename ending, such as sample.ome.tiff or sample.ome.zarr.zip. Renaming a normal TIFF to .ome.tiff, or an arbitrary ZIP to .ome.zarr.zip, does not convert its contents.

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Check OME files before uploading

  • OME-TIFF: export a tiled, single-image file. Supported compression includes uncompressed, LZW, Deflate, PackBits, and JPEG. OME-TIFF using JPEG2000 is not supported, even though supported SVS files may use it.
  • OME-Zarr: use Zarr v2 and put the image store directly at the ZIP root. Do not add an enclosing folder or combine several images into one archive.
  • ZIP packaging: choose Store, also called ZIP_STORED or no compression, for the surrounding archive. Compression inside the Zarr data is separate; not every internal encoding is supported.
  • Channels and image levels: OME images support up to 64 available channels and 32 image levels. You can display up to six channels together. Images must also stay within supported metadata and image-chunk sizes.
If your export does not meet these requirements, create a compatible viewing copy in your image-processing tool and keep the original. Purna does not automatically repair, repack, or convert incompatible slides.

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How your file is prepared

  1. Upload a supported file through Files, or attach it to a conversation. Wait for the upload to finish.
  2. Purna checks that the image is readable and prepares its viewing information, including dimensions, available image levels, channels, and physical scale where supplied.
  3. Open the file to view it. While preparation is pending, the tab shows Preparing viewer… and continues automatically when ready.
New supported uploads prepare automatically. An older file may need preparation when you first open it. Closing the tab does not cancel preparation, and reopening a ready file reuses its prepared viewing information. Your original remains one visible file in Files. Preparation does not overwrite image pixels, change coordinates, infer cell types, detect tissue boundaries, or calculate an analysis. It does not create missing calibration or turn an ordinary image into a compatible slide. Large files can take longer to prepare and open. The viewer loads the image detail needed for your current view as you navigate. Changing zoom or moving to another region can load more detail; a first visit may take longer than revisiting the same area. If preparation fails, the original remains available for download where you still have access. An agent can help investigate the file or write a script for a compatible viewing copy as a separate task. Review any conversion and its assumptions yourself.

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Working with your data

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Open and arrange a slide

Open the file from Files or a chat attachment. On desktop, drag the workspace divider to resize the viewer pane. Use the expand icon for a larger canvas and collapse it to return to your workspace. Use the toolbar to pan, zoom in or out, and fit the image to the available space. Where offered, rotate the slide to inspect it from another orientation. Download the original with the download icon. You can switch between file tabs while working. The viewer retains your current view across tab switches. Wait for Saved before closing or reloading if you have edited a region or its notes.

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Adjust image display

For supported OME images, open the available display controls to choose channels, adjust their colors and intensity ranges, or switch Z and T planes when those dimensions exist. RGB images use their original color mapping. These settings change the display, not the original measurements. A brighter channel or different color does not establish a biological difference. Keep the selected plane and channel settings in mind when comparing regions.

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Select a region

  1. Choose the rectangle or polygon tool.
  2. Draw around the area you want to inspect.
  3. Open Regions and select the region if its details are not already visible.
  4. Enter a meaningful name and optional notes, such as Tissue edge — check staining.
Regions refer to positions in the original image. Zooming, rotating, or resizing the viewer does not move the saved region within the source image. For images with multiple planes, a region also retains its selected plane and display context. The viewer shows region dimensions in pixels. Physical measurements appear only when the source contains valid pixel calibration. Do not infer micrometers from an uncalibrated image.

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Save and revisit regions

Regions save automatically. Use the save icon to save the current edit immediately, and wait for Saved before leaving. The delete icon removes the selected personal region; it does not delete or alter the image. Your named regions, notes, viewport, and supported display settings belong to your personal view of that file. They are not edits to the source or shared annotation editing. Reopen the same file to revisit successfully saved regions. Replacing the source file starts a new view. Regions from the previous file are not automatically transferred to its replacement. Downloading the original does not include your personal regions and notes.

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Select cells when your data supports it

A slide region is an area of an image, not a list of identified cells. Drawing around tissue does not detect, count, label, or segment cells automatically. For prepared datasets with cell identities and coordinates, use the Spatial Omics Viewer. Its available tools can select cells with a lasso, select existing cell groups, and coordinate highlighting across linked views. Those capabilities require prepared cell data; a slide image alone does not supply it.

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Use a region in chat

  1. Select a region and review its name, notes, image plane, and display settings.
  2. Choose Use in Chat.
  3. Choose Start a new chat, or an existing chat in the image’s project. The dialog lists recent chats; type to filter them.
  4. Review the region preview, region-details file, and source-file reference added to the draft.
  5. Add your question and send the message when ready.
Attaching a region does not send a message or start an analysis. Only the selected region’s details are shared; unrelated personal regions are not automatically included. The shared region is a snapshot. If you edit it later, attach a new snapshot when you want the chat to use the revised selection. The source reference identifies the full slide. The selected region covers only a smaller part of it. A region preview is for visual reference and is not a substitute for original values in quantitative work.

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Working with agents

Agents can work with your files and read the selection details you explicitly share, including region coordinates, names, and notes. Use them to help with analysis, statistics, and scripts. They can help check metadata, describe a reproducible analysis, or write code to examine original data. For example, you can ask:
  • “Read the selected region’s coordinates and calibration. Write a script to report its dimensions, and explain any missing information.”
  • “Help me design a comparison between this region and surrounding tissue. List the required measurements and statistical assumptions before calculating anything.”
  • “Check whether this slide contains the channels and metadata needed for my analysis. Do not infer cell identities from the region name.”
Agents cannot view or operate the live graphics or slides in your viewer. They do not share your screen or continuously see your navigation and selections. Sharing selection details or a region preview does not mean an agent has visually reviewed the full slide.Purna is designed to keep a human in the loop. Inspect the slide yourself and verify the selection, source file, measurements, assumptions, statistics, and scripts. Do not rely completely on the agent or treat its response as a validated biological finding or diagnosis.
An agent’s response does not automatically change your image or add regions to the viewer. Give explicit instructions for any separate analysis or conversion you want performed, and review its outputs.

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Limitations and files that will not work

The interactive Slides Viewer is a desktop web feature. Mobile viewing does not provide the same interactive tools. Large images, many channels, and limited browser memory can affect responsiveness even when a file is supported. Automatic segmentation, cell detection, biological interpretation, shared annotation editing, and agent-created viewer overlays are not part of this release.

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Troubleshooting

When contacting support, include the filename, extension, file size, exact error, and the action that failed. Avoid sharing sensitive image contents unless requested through an appropriate support channel. Return to Scientific Components, explore cell-based data in the Spatial Omics Viewer, or see Files for uploading and organizing your data.