I am working with Bruker 2P images, and usually I copy all the channel 2 (gcamp channel) to another folder, and then run suite2p on that. It worked perfectly with the older version, other than an occasional 'too much memory required' error when the images are 1024x1024. This time I have a new error, related to the input and output size. Can I get help resolving this error? Also, I would like to have a separate environment with the old environment, how do I install that?
Here is the error message:
adding F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs to data_path
Running suite2p with command:
python -m suite2p --settings F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs\suite2p\settings.npy --db F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs\suite2p\db.npy --verbose
creating log file F:\2pOpto_AllCa\2pOptoInVivo\04_Full-seq-comp\260609_Y1040_HVCRA_7n\Ind_neuron\s1\Post\01_tifs\suite2p\run.log
2026-06-12 19:12:05,662 [INFO]
cellpose version: 0.99rc0
platform: win32
python version: 3.9.23
torch version: 2.8.0+cpu
2026-06-12 19:12:05,662 [INFO] data_path: ['F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs']
2026-06-12 19:12:05,662 [INFO] ** Found 20 files - converting to binary **
2026-06-12 19:13:09,902 [INFO] Wrote 1000 frames per binary, 1 folders + 1 channels, 64.24sec
2026-06-12 19:13:09,926 [INFO] >>>>>>>>>>>>>>>>>>>>> PLANE 0 <<<<<<<<<<<<<<<<<<<<<<
2026-06-12 19:13:09,926 [INFO] torch.device('cuda') not working, using cpu.
2026-06-12 19:13:09,926 [INFO] Running registration
2026-06-12 19:13:09,926 [INFO] binary output path: F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs\suite2p\plane0\data.bin
2026-06-12 19:13:09,930 [INFO] NOTE: applying default classifier: C:\Users\Roberts_583402.suite2p\classifiers\classifier_user.npy
2026-06-12 19:13:09,933 [INFO] ----------- REGISTRATION
2026-06-12 19:13:09,933 [INFO] registering 1 channels
2026-06-12 19:13:29,889 [INFO] Reference frame, 19.39 sec.
2026-06-12 19:13:29,912 [INFO] Registering 1000 frames in 10 batches
2026-06-12 19:13:29,912 [INFO] 0%| | 0/10 [00:00<?, ?it/s]
2026-06-12 19:13:30,944 [INFO] 0%| | 0/10 [00:01<?, ?it/s]
ERROR: Input and output sizes should be greater than 0, but got input (H: 1, W: 1) output (H: 0, W: 0)
Traceback (most recent call last):
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\gui\rungui_utils.py", line 134, in run
run_s2p(db=db, settings=settings)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\run_s2p.py", line 456, in run_s2p
outputs = run_plane(db=db, settings=settings, db_path=db_path)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\run_s2p.py", line 303, in run_plane
outputs = pipeline(db["save_path"], f_reg, f_raw, f_reg_chan2, f_raw_chan2,
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\pipeline_s2p.py", line 106, in pipeline
reg_outputs = registration.registration_wrapper(
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\register.py", line 896, in registration_wrapper
outputs = register_frames(f_align_in, f_align_out=f_align_out, bidiphase=bidiphase,
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\register.py", line 583, in register_frames
frames = shift_frames(fr_torch, ymax, xmax, ymax1, xmax1, blocks, device)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\register.py", line 444, in shift_frames
fr_torch = nonrigid.transform_data(fr_torch, blocks[2], blocks[1], blocks[0], yoff1, xoff1)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\nonrigid.py", line 413, in transform_data
yxup = F.interpolate(torch.stack((ymax1, xmax1), dim=1),
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\torch\nn\functional.py", line 4774, in interpolate
return torch._C._nn.upsample_bilinear2d(
RuntimeError: Input and output sizes should be greater than 0, but got input (H: 1, W: 1) output (H: 0, W: 0)
error
Interrupted by error (not finished)
I am working with Bruker 2P images, and usually I copy all the channel 2 (gcamp channel) to another folder, and then run suite2p on that. It worked perfectly with the older version, other than an occasional 'too much memory required' error when the images are 1024x1024. This time I have a new error, related to the input and output size. Can I get help resolving this error? Also, I would like to have a separate environment with the old environment, how do I install that?
Here is the error message:
adding F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs to data_path
Running suite2p with command:
python -m suite2p --settings F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs\suite2p\settings.npy --db F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs\suite2p\db.npy --verbose
creating log file F:\2pOpto_AllCa\2pOptoInVivo\04_Full-seq-comp\260609_Y1040_HVCRA_7n\Ind_neuron\s1\Post\01_tifs\suite2p\run.log
2026-06-12 19:12:05,662 [INFO]
cellpose version: 0.99rc0
platform: win32
python version: 3.9.23
torch version: 2.8.0+cpu
2026-06-12 19:12:05,662 [INFO] data_path: ['F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs']
2026-06-12 19:12:05,662 [INFO] ** Found 20 files - converting to binary **
2026-06-12 19:13:09,902 [INFO] Wrote 1000 frames per binary, 1 folders + 1 channels, 64.24sec
2026-06-12 19:13:09,926 [INFO] >>>>>>>>>>>>>>>>>>>>> PLANE 0 <<<<<<<<<<<<<<<<<<<<<<
2026-06-12 19:13:09,926 [INFO] torch.device('cuda') not working, using cpu.
2026-06-12 19:13:09,926 [INFO] Running registration
2026-06-12 19:13:09,926 [INFO] binary output path: F:/2pOpto_AllCa/2pOptoInVivo/04_Full-seq-comp/260609_Y1040_HVCRA_7n/Ind_neuron/s1/Post/01_tifs\suite2p\plane0\data.bin
2026-06-12 19:13:09,930 [INFO] NOTE: applying default classifier: C:\Users\Roberts_583402.suite2p\classifiers\classifier_user.npy
2026-06-12 19:13:09,933 [INFO] ----------- REGISTRATION
2026-06-12 19:13:09,933 [INFO] registering 1 channels
2026-06-12 19:13:29,889 [INFO] Reference frame, 19.39 sec.
2026-06-12 19:13:29,912 [INFO] Registering 1000 frames in 10 batches
2026-06-12 19:13:29,912 [INFO] 0%| | 0/10 [00:00<?, ?it/s]
2026-06-12 19:13:30,944 [INFO] 0%| | 0/10 [00:01<?, ?it/s]
ERROR: Input and output sizes should be greater than 0, but got input (H: 1, W: 1) output (H: 0, W: 0)
Traceback (most recent call last):
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\gui\rungui_utils.py", line 134, in run
run_s2p(db=db, settings=settings)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\run_s2p.py", line 456, in run_s2p
outputs = run_plane(db=db, settings=settings, db_path=db_path)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\run_s2p.py", line 303, in run_plane
outputs = pipeline(db["save_path"], f_reg, f_raw, f_reg_chan2, f_raw_chan2,
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\pipeline_s2p.py", line 106, in pipeline
reg_outputs = registration.registration_wrapper(
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\register.py", line 896, in registration_wrapper
outputs = register_frames(f_align_in, f_align_out=f_align_out, bidiphase=bidiphase,
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\register.py", line 583, in register_frames
frames = shift_frames(fr_torch, ymax, xmax, ymax1, xmax1, blocks, device)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\register.py", line 444, in shift_frames
fr_torch = nonrigid.transform_data(fr_torch, blocks[2], blocks[1], blocks[0], yoff1, xoff1)
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\suite2p\registration\nonrigid.py", line 413, in transform_data
yxup = F.interpolate(torch.stack((ymax1, xmax1), dim=1),
File "C:\Users\Roberts_583402\anaconda3\envs\suite2p\lib\site-packages\torch\nn\functional.py", line 4774, in interpolate
return torch._C._nn.upsample_bilinear2d(
RuntimeError: Input and output sizes should be greater than 0, but got input (H: 1, W: 1) output (H: 0, W: 0)
error
Interrupted by error (not finished)