Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / flatironinstitute/CaImAn issues and pull requests

#1085 - Require param object when initializaing CNMF?

Issue - State: open - Opened by EricThomson over 1 year ago
Labels: type: discussion

#1084 - Buffering and freezing of Vmax/Vmin during motion correction with small file size

Issue - State: closed - Opened by zfyke over 1 year ago - 3 comments
Labels: type: issue with another package

#1083 - Explain how to run CNMF/CNMFE on file that is already motion corrected, not memmapped

Issue - State: open - Opened by EricThomson over 1 year ago - 2 comments
Labels: type: feature request, status: under development

#1082 - automated parameter optimization ideas

Issue - State: open - Opened by kushalkolar over 1 year ago

#1081 - remove reference to old mesmerize in docs

Pull Request - State: closed - Opened by kushalkolar over 1 year ago

#1080 - Embed opencv

Pull Request - State: closed - Opened by j-friedrich over 1 year ago - 5 comments

#1079 - Running out of Memory and Motion Correction patches moving separately.

Issue - State: closed - Opened by JLRomero12 over 1 year ago - 16 comments
Labels: type: question

#1078 - Sparse nmf debugging

Pull Request - State: closed - Opened by EricThomson over 1 year ago - 1 comment
Labels: type: bug fix

#1077 - Can't install caiman

Issue - State: closed - Opened by rosullivan1226 over 1 year ago - 9 comments
Labels: type: build/install/tests

#1076 - IndexError while using sparse_nmf initialization method on demo_dendritic.ipynb

Issue - State: closed - Opened by KunyunWang over 1 year ago - 5 comments
Labels: type: bug

#1075 - CNMF notebook update

Pull Request - State: open - Opened by EricThomson almost 2 years ago - 11 comments

#1074 - Notebook Demo Error

Issue - State: closed - Opened by ambtetl almost 2 years ago - 3 comments
Labels: type: issue with another package

#1073 - Pass file list to load_iter

Issue - State: closed - Opened by Marekthegeck almost 2 years ago - 2 comments
Labels: type: question

#1072 - evaluate_components crashes when using non-integer gSig

Issue - State: open - Opened by oterocoronel almost 2 years ago - 6 comments
Labels: type: discussion

#1071 - How to pass var_name_hdf5 when running mcorr

Issue - State: closed - Opened by oterocoronel almost 2 years ago

#1070 - OnACID docs

Pull Request - State: closed - Opened by kushalkolar almost 2 years ago - 4 comments
Labels: status: under review

#1069 - dev to master for release

Pull Request - State: closed - Opened by EricThomson almost 2 years ago

#1068 - Setting nb and nb_patch to 0 or negative values results in crash

Issue - State: open - Opened by oterocoronel almost 2 years ago - 2 comments
Labels: type: bug, status: awaiting user response

#1067 - Volpy notebook

Pull Request - State: closed - Opened by caichangjia almost 2 years ago - 7 comments

#1066 - remove all python2 relics such as old_div

Pull Request - State: closed - Opened by j-friedrich almost 2 years ago

#1065 - spatial_update with ellipse crashes for large 4D recording

Issue - State: open - Opened by oterocoronel almost 2 years ago - 3 comments
Labels: type: bug, status: under investigation

#1064 - play_movie error

Issue - State: closed - Opened by nizheyi almost 2 years ago - 10 comments
Labels: type: bug, status: awaiting user response

#1062 - online processing of volumetric data

Pull Request - State: closed - Opened by j-friedrich almost 2 years ago - 1 comment

#1061 - Cannot find min_size and max_size in cnmf.params

Issue - State: closed - Opened by oterocoronel almost 2 years ago - 2 comments

#1060 - Enhancing dot product for sparse matrices during ROI spatial updating

Issue - State: open - Opened by oterocoronel almost 2 years ago - 1 comment
Labels: type: bug, status: under investigation

#1059 - Q about differences in results using batch and online methods

Issue - State: closed - Opened by XiaoqianSun0104 almost 2 years ago - 7 comments

#1058 - CNMF seems to be merging components despite setting do_merge = False

Issue - State: open - Opened by oterocoronel almost 2 years ago - 1 comment
Labels: type: bug, status: under investigation

#1057 - Caiman not found M1 Mac

Issue - State: closed - Opened by ambtetl almost 2 years ago - 6 comments
Labels: type: issue with another package

#1056 - Python 3.11 build

Issue - State: closed - Opened by rob-the-bot almost 2 years ago - 8 comments

#1055 - correlation_pnr fails on 4D arrays

Issue - State: closed - Opened by oterocoronel almost 2 years ago - 3 comments

#1054 - add related packages and videos to README

Pull Request - State: closed - Opened by kushalkolar almost 2 years ago

#1053 - Dev to master for release

Pull Request - State: closed - Opened by pgunn almost 2 years ago

#1052 - 1p Motion Correction

Issue - State: closed - Opened by yunip20 almost 2 years ago - 2 comments

#1051 - Conda installation installs incompatible version of pynwb

Issue - State: closed - Opened by rly almost 2 years ago - 5 comments
Labels: type: build/install/tests

#1050 - Cannot set up caimanmanager

Issue - State: closed - Opened by cyberfag almost 2 years ago - 5 comments
Labels: type: build/install/tests, status: awaiting user response

#1049 - unresponsive cells in demo_pipeline_cnmfE

Issue - State: closed - Opened by dprotter almost 2 years ago - 5 comments

#1047 - Motion Correction: IndexError

Issue - State: closed - Opened by ggmirandac almost 2 years ago - 5 comments

#1046 - Caimanmanager.py install fail

Issue - State: closed - Opened by Sky-ShiKeyue almost 2 years ago - 1 comment

#1045 - 3D non-rigid motion correction crashes with multi-file recordings

Issue - State: closed - Opened by oterocoronel almost 2 years ago - 2 comments

#1044 - ImportError: The 'platformdirs' package is required

Issue - State: closed - Opened by njm94 almost 2 years ago - 4 comments

#1043 - demo for running OnACID in realtime

Issue - State: open - Opened by kushalkolar almost 2 years ago - 3 comments
Labels: type: feature request

#1042 - Online motion correction + save templates over time

Pull Request - State: closed - Opened by RuiOSilva almost 2 years ago

#1041 - Open multiseries tiff files and nd2 files

Pull Request - State: closed - Opened by RuiOSilva almost 2 years ago - 6 comments

#1040 - Changed load functions

Pull Request - State: closed - Opened by RuiOSilva almost 2 years ago

#1039 - implement type checks and better error messages when creating `CNMFParams`

Issue - State: open - Opened by kushalkolar almost 2 years ago - 1 comment
Labels: type: feature request

#1038 - Save and visualize motion correction templates while code is running

Issue - State: closed - Opened by RuiOSilva almost 2 years ago - 4 comments

#1037 - Save lower resolution .mmap files?

Issue - State: open - Opened by RuiOSilva almost 2 years ago - 5 comments
Labels: type: feature request, status: under investigation

#1036 - Better error when using data with less than 200 frames for mcorr

Issue - State: open - Opened by kushalkolar about 2 years ago - 2 comments
Labels: type: feature request, status: under development

#1035 - DF_F extraction

Issue - State: closed - Opened by ggmirandac about 2 years ago - 2 comments

#1034 - decode mmap logging is noisy

Issue - State: closed - Opened by kushalkolar about 2 years ago - 9 comments
Labels: type: feature request, status: under development

#1033 - Use own data to analyze

Issue - State: closed - Opened by ggmirandac about 2 years ago - 3 comments

#1032 - Running Caiman GUI on 1p Data

Issue - State: closed - Opened by jljavie about 2 years ago - 4 comments

#1031 - remove duplicate question in ISSUE_TEMPLATE

Pull Request - State: closed - Opened by kushalkolar about 2 years ago

#1030 - certificate expired when trying download_demo()

Issue - State: closed - Opened by happyqiu about 2 years ago - 9 comments
Labels: type: bug

#1029 - 'CNMF' object has no attribute '_prepare_object'

Issue - State: closed - Opened by XiaoqianSun0104 about 2 years ago - 9 comments

#1028 - Update initialization.py

Pull Request - State: closed - Opened by IshraqFARHAN about 2 years ago - 4 comments

#1027 - Update initialization.py

Pull Request - State: closed - Opened by IshraqFARHAN about 2 years ago

#1026 - Dev to master for release 1.9.13

Pull Request - State: closed - Opened by pgunn about 2 years ago

#1025 - change np.int->int, np.float->float, np.bool->bool, np.object->object…

Pull Request - State: closed - Opened by j-friedrich about 2 years ago - 1 comment

#1024 - `numpy.int` deprecation has expired and now throws an error

Issue - State: closed - Opened by kushalkolar about 2 years ago - 1 comment

#1023 - Fix volpy bug

Pull Request - State: closed - Opened by caichangjia about 2 years ago - 1 comment

#1022 - sklearn deprecation, remove `normalize` from LassoLars

Pull Request - State: closed - Opened by kushalkolar about 2 years ago - 1 comment

#1021 - which `nose` is required to run `caimanmanager.py test`

Issue - State: closed - Opened by kushalkolar about 2 years ago - 2 comments
Labels: type: build/install/tests

#1020 - Caiman not working well on linux mint 21

Issue - State: closed - Opened by aidanortega about 2 years ago - 9 comments

#1019 - ModuleNotFoundError: No module named 'caiman'

Issue - State: closed - Opened by ambtetl about 2 years ago - 23 comments
Labels: type: issue with another package

#1018 - dev -> master for release

Pull Request - State: closed - Opened by pgunn about 2 years ago

#1016 - Out of memory with demo_pipeline_cnmfE.py

Issue - State: open - Opened by restrepd over 2 years ago - 9 comments
Labels: type: question

#1015 - tensorflow-gpu install conflicts on fresh CaImAn install

Issue - State: closed - Opened by BptGrm over 2 years ago - 4 comments
Labels: type: bug, status: awaiting user response

#1014 - mmapping paths: rework parsing of filenames

Pull Request - State: closed - Opened by pgunn over 2 years ago - 7 comments

#1013 - VolPy Mask_RCNN does not work in CaImAn 1.9.9 or later

Issue - State: closed - Opened by KawashimaLab over 2 years ago - 6 comments

#1012 - caimanmanager.py install fail

Issue - State: closed - Opened by katesal327 over 2 years ago - 21 comments
Labels: type: bug

#1011 - num_frames_split not used in caiman.motion_correction.py

Issue - State: closed - Opened by flmuk over 2 years ago - 2 comments

#1010 - Running CAIMAN on large movies

Issue - State: closed - Opened by fatihdinc over 2 years ago - 7 comments

#1009 - Intel CPUs required?

Issue - State: closed - Opened by r5r3 over 2 years ago - 3 comments

#1008 - After running demo_pipeline, the result just quitted unexpectedly

Issue - State: closed - Opened by ykmcheng over 2 years ago - 1 comment

#1007 - Issue saving `cnn_preds` when CNMF params tuned for dendrites

Issue - State: open - Opened by kushalkolar over 2 years ago - 1 comment
Labels: type: bug

#1001 - Tracking bug: VSCode's "Jupyter mode" does not support all Jupyter UI in caiman

Issue - State: open - Opened by pgunn over 2 years ago - 3 comments
Labels: type: bug, type: tracking issue

#999 - Negative spatial correlation

Issue - State: closed - Opened by MarziyehPourmousavi over 2 years ago - 1 comment
Labels: type: question

#997 - API docs not rendering

Issue - State: open - Opened by kushalkolar over 2 years ago - 3 comments
Labels: type: bug, type: documentation

#991 - Volpy GUI unable to load summary images

Issue - State: closed - Opened by cawarwick over 2 years ago - 4 comments

#988 - Ideas about storage engine

Issue - State: open - Opened by kushalkolar over 2 years ago - 2 comments
Labels: type: discussion

#987 - Temporal components with negative values (in estimates.C)

Issue - State: closed - Opened by NataliaFavila over 2 years ago - 7 comments
Labels: status: under discussion

#986 - Index out of bounds

Issue - State: closed - Opened by clay34207 over 2 years ago - 9 comments

#984 - Rerun with the same options bug

Issue - State: open - Opened by fatihdinc over 2 years ago - 2 comments
Labels: type: bug, status: under development

#983 - Error with save_memmap

Issue - State: closed - Opened by fatihdinc over 2 years ago - 3 comments
Labels: type: bug

#976 - error when use caiman_gui.py after running demo_pipeline.py

Issue - State: closed - Opened by J0eky over 2 years ago - 3 comments
Labels: type: bug

#972 - Unit tests fail to run due to problem with nose

Issue - State: closed - Opened by GBarnum over 2 years ago - 5 comments
Labels: type: bug

#965 - volpy maskrcnn compatible tensorflow 2.4.1

Pull Request - State: closed - Opened by caichangjia almost 3 years ago

#961 - import error

Issue - State: closed - Opened by bendichter almost 3 years ago - 11 comments
Labels: type: bug

#948 - Save results to a user given output directory

Pull Request - State: open - Opened by tdincer almost 3 years ago - 10 comments

#944 - update to keep data as float32

Pull Request - State: closed - Opened by JakeHeffley about 3 years ago - 2 comments

#921 - estimates.F_dff baseline negative

Issue - State: closed - Opened by jorareshuaiwang over 3 years ago - 4 comments
Labels: type: question

#916 - Repository contains large, binary, files

Issue - State: closed - Opened by orpinchasov over 3 years ago - 7 comments
Labels: type: discussion

#910 - pynwb 2.0.0 creates troubles

Issue - State: closed - Opened by agiovann over 3 years ago - 2 comments

#903 - Running volpy on linescans

Issue - State: closed - Opened by m-bellv over 3 years ago - 1 comment

#902 - cannot import name 'file_hash' from 'pooch.utils'

Issue - State: closed - Opened by obarnstedt over 3 years ago - 3 comments