CellCounter 1.0.8 (macOS)

CellCounter 1.0.8 for macOS — native Apple Silicon and Intel universal build. Requires macOS 15 or later.

This release fixes vendor microscopy imports and the six macOS workflow issues reported against 1.0.7, while substantially reducing latency on large datasets.

Vendor microscopy formats

• .nd2, .czi, .lif, .oif, .oib, and .oir now pass every native import entry point instead of being silently filtered out.
• Vendor containers are retained as the source of truth and prepared through the Python image reader into a lossless display image plus thumbnail for native overlays and exports.
• Dimensions, channels, Z/T metadata, and physical calibration are carried into the native record when available.
• Vendor-reader selection follows the installed model family and reports an actionable error when a required reader is unavailable.

Batch export, calibration, and presentation

• Download batch now exports every annotated image as PNG in a single operation.
• Export folders use the batch name, safely normalized for macOS paths.
• Analyzed batches keep their persisted calibration; changing the Home default only affects future analysis.
• Corrected the exported-image orientation so masks and scale bars are no longer mirrored.
• Cell-bin and overlay colors are customizable for bright, dark, and low-contrast fields.
• Calibration is detected from supported image metadata and applied consistently to physical measurements and scale bars.

Performance

• Detection payloads, thumbnails, full-resolution viewer images, and review previews use bounded caches instead of repeated disk/JSON decoding.
• Annotation matching, sequence drift estimation, and mask propagation use spatial indexes rather than quadratic full-field scans.
• Batch insights, comparison statistics, CSV preparation, folder discovery, hashing, and export preparation run away from the UI thread.
• Imports and bulk deletion use batched persistence, and concurrent comparison consumers share one pooled analysis.
• The 2,500-cell interaction benchmark dropped from 41.4 seconds to about 0.24 seconds, over 170× faster.

Validation

• 14 macOS unit tests pass, including large-workload performance budgets.
• 2 vendor-image preparation tests pass.
• The release archive is a universal arm64 + x86_64 binary and passes strict code-signature validation.
• ZIP SHA-256: cbc72cd5c573ef96dca9da260d90c30ba7395a56088f510c10a9a8e45043d593

Upgrading

Replace the application. Existing images, batches, masks, corrections, and model environments remain in place.

Install

1. Download CellCounter-v1.0.8.zip, unzip it, and move CellCounting.app into Applications. The product is CellCounter; the application bundle is still named CellCounting.app.
2. The app is not notarized, so macOS may block the first launch. Open System Settings → Privacy & Security, scroll to the bottom, and select Open Anyway. If macOS reports that the app is damaged, run xattr -cr /Applications/CellCounting.app in Terminal.
3. On first use, open the Models tab and install the model you need. Model environments and weights are downloaded separately.

Full walkthrough: docs/INSTALL.md

Fixes #7 and #8.