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Updating the segmentation to use Cellpose SAM

Status: Open (in progress).

czbiohub-sf/biahubnumber 101

#101 In czbiohub-sf/biahub;

· edyoshikun opened on Jun 16, 2025

<code>characterize-psf</code> with larger datasets

Status: Open (in progress).

czbiohub-sf/biahubnumber 62

#62 In czbiohub-sf/biahub;

· talonchandler opened on Mar 18, 2025

Correct distortion as estimated with discorpy

Status: Draft (not ready).

czbiohub-sf/biahubnumber 39

#39 In czbiohub-sf/biahub;

· ieivanov opened on Feb 5, 2025

Compute per patch stats

Status: Draft (not ready).

czbiohub-sf/biahubnumber 109

#109 In czbiohub-sf/biahub;

· edyoshikun opened on Jul 23, 2025

CLI option to specify a time point indices for registration

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#136 In czbiohub-sf/biahub;

· srivarra opened on Aug 11, 2025

Filling overhang region with zeros creates labelfree reconstruction artifacts

deskewDeskewing light-sheet fluorescence volumesDeskewing light-sheet fluorescence volumes

enhancementNew feature or requestNew feature or request

Status: Open.

#118 In czbiohub-sf/biahub;

· talonchandler opened on Aug 1, 2025

Support 2D affine transforms

Status: Open.

#117 In czbiohub-sf/biahub;

· tayllatheodoro opened on Aug 1, 2025

Enable registration with sobel filters from multiple channels

Status: Open.

#114 In czbiohub-sf/biahub;

· ieivanov opened on Jul 29, 2025

Overhaul registration and stabilization

Status: Open.

#89 In czbiohub-sf/biahub;

· ieivanov opened on May 13, 2025

Use 3D phase cross correlation for 3D stabilization

Status: Open.

#65 In czbiohub-sf/biahub;

· ieivanov opened on Apr 1, 2025

Move <code>biahub deconvolve</code> to <code>waveorder</code>

Status: Open.

#63 In czbiohub-sf/biahub;

· talonchandler opened on Mar 26, 2025

Improving stabilization over time like autotracker

Status: Open.

#28 In czbiohub-sf/biahub;

· edyoshikun opened on Dec 6, 2024

Stabilization refactoring

Status: Open.

#54 In czbiohub-sf/biahub;

· edyoshikun opened on Mar 8, 2025

Unify registration and stabilization pipelines

Status: Open.

#38 In czbiohub-sf/biahub;

· ieivanov opened on Jan 22, 2025

Hardcoded focus finding variables in stabilization algorithm

Status: Open.

#72 In czbiohub-sf/biahub;

· edyoshikun opened on Jul 2, 2024