From 17b4d2cf07af18a427970ef8c074159c3f295048 Mon Sep 17 00:00:00 2001 From: Michael Rariden Date: Mon, 9 Jun 2025 16:26:17 -0400 Subject: [PATCH] read image as 3d if stitch_threshold > 0 --- cellpose/__main__.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cellpose/__main__.py b/cellpose/__main__.py index 25cd58a0..f50d2497 100644 --- a/cellpose/__main__.py +++ b/cellpose/__main__.py @@ -206,7 +206,8 @@ def _evaluate_cellposemodel_cli(args, logger, imf, device, pretrained_model, nor z_axis = args.z_axis for image_name in tqdm(image_names, file=tqdm_out): - if args.do_3D: + if args.do_3D or args.stitch_threshold > 0.: + logger.info('loading image as 3D zstack') image = io.imread_3D(image_name) if channel_axis is None: channel_axis = 3