Closed bobonannan closed 4 days 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
I think this might be fixed now, try installing the latest version pip install git+https://github.com/mouseland/cellpose.git
pip install git+https://github.com/mouseland/cellpose.git
closing for now, will reopen if it's not working
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