MouseLand / cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
https://www.cellpose.org/
BSD 3-Clause "New" or "Revised" License
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[BUG]In windows ,I can not save outlines as.zip archive of ROI files for imajej #1006

Closed bobonannan closed 4 days ago

bobonannan commented 1 week ago

GUI_INFO: normalization checked: computing saturation levels (and optionally filtered image) {'lowhigh': None, 'percentile': [1.0, 99.0], 'normalize': True, 'norm3D': False, 'sharpen_radius': 0, 'smooth_radius': 0, 'tile_norm_blocksize': 0, 'tile_norm_smooth3D': 1, 'invert': False} [0, 255.0] (1, 1024, 1024, 1) GUI_INFO: 4532 masks found GUI_INFO: creating cellcolors and drawing masks GUI_INFO: loaded in previous changes GUI_INFO: saving 4532 ImageJ ROIs to .zip archive. 2024-09-03 17:44:35,645 [WARNING] Multiprocessing is disabled for Windows Traceback (most recent call last): File "D:\anaconda\envs\cellpose\lib\site-packages\cellpose\gui\menus.py", line 62, in parent.saveROIs.triggered.connect(lambda: io._save_rois(parent)) File "D:\anaconda\envs\cellpose\lib\site-packages\cellpose\gui\io.py", line 590, in _save_rois save_rois(parent.cellpix[0], parent.filename) File "D:\anaconda\envs\cellpose\lib\site-packages\cellpose\io.py", line 592, in save_rois rois = [ImagejRoi.frompoints(outline) for outline in outlines] File "D:\anaconda\envs\cellpose\lib\site-packages\cellpose\io.py", line 592, in rois = [ImagejRoi.frompoints(outline) for outline in outlines] File "D:\anaconda\envs\cellpose\lib\site-packages\roifile\roifile.py", line 455, in frompoints left_top = coords.min(axis=0) File "D:\anaconda\envs\cellpose\lib\site-packages\numpy\core_methods.py", line 45, in _amin return umr_minimum(a, axis, None, out, keepdims, initial, where) ValueError: zero-size array to reduction operation minimum which has no identity

I segment 4532 mask ,but I want get cell area in imajej ,but i can not save it

carsen-stringer commented 1 week ago

I think this might be fixed now, try installing the latest version pip install git+https://github.com/mouseland/cellpose.git

carsen-stringer commented 4 days ago

closing for now, will reopen if it's not working