VIPP 0.15.0a5¶
VIPP 0.15.0a5 adds a colocalization mask for counting overlap regions, clearer guided examples, and simpler desktop launching and updates. It also improves inspector histograms and keeps mesh-display warnings compact.
Find and explore an example¶
The example chooser now has a searchable list and resizable detail panel. All 22 examples explain their input data, what to explore, what you will get, and one thing to try. Short bullet lists and interpretation notes make the choices easier to scan. Developer/testing workflows are grouped separately; browsing does not calculate images.
The catalogue's graph layouts have clearer spacing between nodes, tunnels and notes. The former combined colocalization example is now two focused examples:
- RACC Colocalization explains the method and links its original paper. Both index maps use Magma, manual channel thresholds of 43,970.51 and 48,073.03, and a red-channel region cutoff of 30,000.
- Colocalization, Overlap & Object Counts compares whole-image and region-restricted overlays and metrics, then cleans, labels and measures connected overlap regions.
These are sample-specific settings. Reopen an example to get its revised layout; your saved workflows are not rearranged or retuned automatically.
Turn overlap into a measurable mask¶
Colocalization Mask outputs a true Boolean mask where both channels are at or above their respective thresholds. Choose native-intensity Manual cutoffs or whole-image Costes auto, then connect cleanup, connected-component labelling and object measurements. The mask retains axes and calibration and matches the white overlap of the unmasked voxel overlay at the same thresholds.
Counts describe connected overlap regions, not necessarily whole organelles or biological events. A downstream Logical AND can restrict the mask to a region, but does not change the population used to estimate Costes thresholds. See segment and count overlap regions.
Simpler desktop use¶
- Open one VIPP shortcut/app on Windows or macOS. It starts in Auto; other compute choices remain inside VIPP. GPU dependencies are still an installation capability, not a separate app icon.
- With automatic checks enabled, VIPP checks for updates on every startup. The clearer update dialog distinguishes fresh results, connection problems and cached release information.
- Verified managed Windows installations offer Download & open update: download the official installer, verify its checksum, and open guided setup for the current installation. Setup still needs review; the action does not silently replace a live environment, close unsaved work or restart VIPP. macOS and manually managed environments retain their browser/manual routes.
Clearer inspection¶
The Intensity Histogram inspector grows vertically to fit its plot, labels and wrapped channel legend at narrow widths or larger fonts. Histogram values, pop-out plots and exports are unchanged. Mesh inspection avoids unnecessary calibration resets; a display failure now shows a short warning with Details… and Dismiss, without discarding the calculated result.
Install and compatibility¶
Use the canonical GitHub release for installers, matching checksums and qualification evidence, or the exact PyPI version. Windows and the separate Apple Silicon/Intel macOS installers remain unsigned; macOS packages are also unnotarized and CPU-only. Follow the installation instructions.
Installation temporarily requires psygnal>=0.14,<0.16 to avoid mesh/crop
display failures reproduced with psygnal 0.16.0.
Workflow, batch-config and manifest schemas remain 6. Workflows using Colocalization Mask require a runtime containing that node; unchanged schema numbers do not make it available in older VIPP versions. Regenerate Python exports for the installed version and recheck consequential analyses.
The qualification declaration separates changed-domain checks from carried-forward evidence. The new mask runs on CPU; this release does not broaden GPU execution policy or establish independent biological validation.