Learn SlideScope

Get from installed to real results

Every guide below is a task somebody actually needs to finish, with an honest time estimate and three steps. Start with the path if SlideScope is new to you, or jump straight to the job in front of you.

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CZI · ND2 · SVS · DICOM · TIFFWindows · macOSSlideScope 1.8.5

Start here

About ten minutes, once. Do these in order and everything else on this page will make sense.

  1. Install and activate

    Download the signed build for Windows or macOS and sign in with the account you used for the trial or subscription. Activation binds to the machine, and one subscription covers two devices, so your laptop and your workstation can both stay signed in.

  2. Open your first slide

    Drag a CZI, ND2, SVS, NDPI, DICOM or TIFF file onto the window. There is no import step and no conversion: SlideScope reads the scanner pyramid directly, so a gigapixel slide opens on an ordinary laptop.

  3. Find your way around

    Scroll to zoom, drag to pan, and use the overview navigator to jump across the slide without losing your place. Check the metadata panel early: the pixel size recorded there is what makes every later measurement calibrated rather than approximate.

Guides by task

Pick the one that matches what you are trying to do today.

Count nuclei in a fluorescence image

6 min
  1. Open the image and select the region you want counted. Quantifying a region rather than a whole slide keeps the run fast and keeps the result on the tissue you care about.
  2. In the Quantify panel choose Nuclei, pick InstanSeg as the engine, and set the segmentation channel to your DAPI or nuclear stain. Leave the advanced settings alone on the first run.
  3. Run it, then read the overlay before you read the number. Click any object that looks wrong and exclude it, then export the CSV and the methods summary together.

Measure a structure in micrometres

4 min
  1. Confirm the metadata panel shows a pixel size. If the scanner recorded one, measurements come out in real micrometres; if it did not, calibrate manually before measuring anything.
  2. Choose the measurement tool and draw across the structure. Distances and areas are computed at full slide resolution, not at whatever zoom level you happen to be viewing.
  3. Save the measurement so it stays attached to the slide, then export the table as CSV or the regions as GeoJSON when you need them elsewhere.

Compare H&E against its IHC restain

5 min
  1. Open the first slide, then open the second one beside it. Both panes lock to the same part of the tissue at the same magnification.
  2. Scale is matched in micrometres rather than by zoom factor, so two scans digitised at different resolutions genuinely correspond. Pan or zoom either pane and the other follows.
  3. Annotate on whichever pane makes sense. Notes stay attached to their own slide and to your account, so the next reviewer sees them.

Quantify an entire folder in one run

8 min
  1. Get one image right first. Tune the object type, engine, channel and area limits on a single representative image until the overlay looks correct.
  2. Save those settings as a recipe and give it a name you will recognise in three months.
  3. Choose Folder batch, point it at the directory, and let it run. You get per-image exports plus a combined batch summary CSV, with every image analysed by identical settings.

Share the exact view you are looking at

3 min
  1. Navigate to the field of view you want the other person to see, at the zoom and plane you want them to see it.
  2. Create a shared view link. It carries the slide together with position, zoom and plane, so they do not have to hunt across a gigapixel scan.
  3. Send it. Anyone with SlideScope installed opens it in one click through the slidescope:// handler; anyone without it sees what the link points at on the website first.

Reference

Keep these open in a tab while you work.

Quantifysupported file formatsTrust and data handlingContactRelease Notes

FAQ

I am completely new to this. Where do I start?

Work through the three start-here steps in order, then do the measurement guide. Those four things cover most of what a new user needs in the first week. The counting guide is worth doing next even if you do not think you need quantification yet, because it is the fastest way to understand how SlideScope treats calibration.

Do I need to learn any scripting?

No. Nothing on this page requires a script, a macro, a plugin or a Python environment. Quantification is driven by saved recipes rather than code, which is the trade: less flexible than a programmable platform, far quicker to get a result from.

How do I train other people in my lab?

Send them a shared view link pointing at a real slide from your own work, together with this page. Opening something familiar beats a synthetic tutorial file, and the link means they see the same field of view you did rather than a different corner of the scan.

Learn it on your own images

The 14-day trial is full access. Work through these guides using the slides your laboratory is actually dealing with, not a sample file.

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supported file formatsRelease NotesAlternativesTrust and data handling