Slide Reader · User Guide

Language Choose Settings → Interface Language. Follow System or select a language. Quit and reopen the app to apply it; changing the preference does not interrupt current work. Case titles and filenames are never translated. Getting started Open Slides accepts compatible KFB files and PNG, JPEG, TIFF, BMP or WebP images. You may choose a folder; only its immediate contents are included. Choose a reference slide and create a case. Images open immediately in their original positions. Start Alignment estimates translation, rotation and scale; it does not perform elastic registration. You can leave the canvas while alignment continues. Cancel keeps completed results. Interrupted alignment attempts to resume on the next launch. Wait for cancellation to finish before deleting a case. Help → Open Synthetic Example provides generated textures without patient data. It demonstrates operation, not diagnostic or clinical accuracy. Comparison and manual alignment Blend overlays visible layers with adjustable opacity. Curtain compares the reference and another slide across a draggable divider. Spotlight reveals the reference in a circle under the pointer. Drag rows to reorder layers. Hold a number key to hide its visible layer temporarily; hold Space to show only the reference. Scroll or zoom with the trackpad; ⌘0 resets the view. Enable Align This Slide Manually. Drag to move, ⌥-drag to rotate and ⌘-drag to scale around the slide center. Arrow keys move, comma/period rotate, brackets scale; ⇧ increases the step. Numeric fields express offsets relative to automatic alignment; all zeros restore that position. Save Alignment writes manual.json without changing computed alignment. Revert This Slide or Revert All discards manual adjustments, restoring computed positions (or original positions if not aligned). Manual changes do not alter structural correlation scores. Region cell analysis Open Region Cell Analysis from the sidebar or File menu. Select a slide. Freehand closes when you release the pointer. For Polygon, click vertices and double-click or press Return to close; Backspace removes a vertex and Esc cancels. Name multiple regions and switch between them with the region picker. Click Start Analysis. Ki67 detects objects by stain optical density and assigns A (positive/dark) or B (negative/light) using mean DAB concentration. Grayscale uses mean optical density. Negative means detected lightly stained nuclei, not blank background. Lower detection thresholds find lighter objects but can merge background. Set minimum/maximum area in original-image px²; calibrated results also display µm². Parameters and counting changes require reanalysis, which resets group corrections. Count Connected Objects as One uses 4- or 8-connectivity. Disable it to split touching objects and count them separately; connectivity then has no effect. White lines show splits without subtracting area. Splitting estimates visible individuals and may over- or under-separate irregular, blurred or overlapping objects; it cannot recover fully occluded cells. Verify against the original image. Area means detected object pixels, not complete cell outlines. Filtering and boundary exclusion apply per object after splitting; totals may change with the counting method. Boundary objects are included by default, counting only their part inside the region. Exclude Objects Touching the Boundary removes them. Detection does not identify tumor cells; outline the intended region and exclude unwanted cells manually. Click objects or drag a selection box (based on object centers); ⌘/⇧ extends selection. The table also supports multiple selection and double-click to locate. Assign A, B or Excluded; undo up to 20 group changes. Exclude All lets you build two comparison groups manually. Orange is A, blue B, yellow selected. Results show A/B count and area ratios and A/(A+B). Excluded objects are omitted; zero denominators show “—”. Regions are independent: overlap is not deduplicated. Original resolution is recommended; lower resolutions may merge or miss small objects. Limits are 16 million analysis pixels and 50,000 objects per region. Oversized regions require explicit adjustment, never silent downsampling. Analysis runs in the background and can be cancelled. Regions, parameters, pixel geometry and corrections are saved locally in cell-analysis.json. Old records retain connected-object counting. Export All Regions as CSV includes summaries, objects and parameters in the chosen language; numeric values use a dot decimal separator for interchange. Existing results retain the parameters shown beneath them. Files, export and limitations Cases reference original files without copying or modifying them. If files move, a disk disconnects or permission expires, reselect the same originals. If their contents changed, create and align a new case. File exports the current view or window as PNG and alignment as JSON. Exports are managed in your chosen location. Ordinary TIFF reads only its first frame. This is not a universal SVS/NDPI or multi-page whole-slide TIFF reader. KFB compatibility varies by version. Images without physical calibration use pixels, not real-world measurements. Serial sections can differ through stretching, tissue loss or folds. Check each region manually. Structural correlation is not diagnostic accuracy or disease probability. Hidden unmatched slides can be shown again. Do not infer cell identity or make medical decisions from overlay alone. This app is for teaching and research comparison; it does not provide automated diagnosis, lesion detection or treatment advice. Clinical decisions require qualified professionals and appropriate validation. Processing is local, without an account or network access. See Help → Privacy Policy.