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fractal-analytics-platform / fractal-tasks-core

Main tasks for the Fractal analytics platform
https://fractal-analytics-platform.github.io/fractal-tasks-core/
BSD 3-Clause "New" or "Revised" License
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Cellpose task doesn't handle 2D MD data anymore #520

Closed jluethi closed 11 months ago

jluethi commented 12 months ago

The issue comes from here: https://github.com/fractal-analytics-platform/fractal-tasks-core/blob/cafe063f2a46355e529f914ea7c2f2ec9fe9cbd0/fractal_tasks_core/tasks/cellpose_segmentation.py#L435

We create the new label dataset based on the attributes of the image dataset. But MD image datasets will be yx (for the 2D case), while the output that the cellpose task generates will be zyx (also for the 2D case).

Another instance of https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/150

Apparently, our most recent changes to cellpose broke the (admittedly somewhat hacky) solution we implemented in https://github.com/fractal-analytics-platform/fractal-tasks-core/pull/403

cc @fstur

jluethi commented 12 months ago

(we'll need to re-evaluate this bug report. We had an issue with MD ROIs having y & x shifted. But I'm still suspicious that the thing above could be going wrong)

jluethi commented 12 months ago

Never mind, it actually works as expected 🙈 (once we have the ROI bug fixed, see fractal-faim-hcs package)