flatironinstitute/CaImAn issues and pull requests

#1203 - Switch from the z5py library to the zarr library

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

#1202 - remove relative imports, generally clean up imports, remove dead code

Pull Request - State: open - Opened by pgunn over 1 year ago - 2 comments

#1200 - Unable to us cnm.load() after cnm.save

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 2 comments
Labels: type: question

#1199 - Caiman version on windows

Issue - State: closed - Opened by noah-chongsiriwatana over 1 year ago - 20 comments
Labels: type: build/install/tests

#1198 - Error when saving OnACID object

Issue - State: open - Opened by StoyoKaramihalev over 1 year ago - 1 comment
Labels: type: bug

#1194 - get_file_size move

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

#1193 - How to get cell x/y coordinates

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 1 comment

#1192 - Movie save for avi in Windows doesn't work

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

#1191 - fix `scipy.ndimage` namespace deprecations and some invalid escape sequences in docstrings

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

#1189 - Running caiman in google cloud

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 30 comments
Labels: type: build/install/tests

#1188 - estimates.detrend_df_f use_residuals keyword has no effect

Issue - State: open - Opened by EricThomson over 1 year ago - 4 comments
Labels: type: bug

#1187 - Issues with win installation. Cant install caimanmanager in env

Issue - State: closed - Opened by Jorgenhoyer over 1 year ago - 5 comments

#1186 - add check for rf and gSiz

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

#1185 - Cryptic errors when CNMFE params are incompatible

Issue - State: open - Opened by kushalkolar over 1 year ago - 10 comments
Labels: type: bug

#1184 - Very high RAM usage in demo_pipeline.ipynb

Issue - State: closed - Opened by salehtahini over 1 year ago - 2 comments
Labels: type: question

#1183 - WIP: py39

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

#1182 - dev->main for release 1.9.16

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

#1181 - main->dev before dev->main

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

#1180 - cell is sliding and how can I exclude it?

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 3 comments
Labels: type: question

#1179 - Allows overriding of opencv default for avi files

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

#1177 - Final poking and prodding before release

Pull Request - State: closed - Opened by EricThomson over 1 year ago - 2 comments

#1171 - Issues with detrend_df_f

Issue - State: closed - Opened by JLRomero12 over 1 year ago - 10 comments
Labels: type: question

#1170 - Adjust the CNMF-E parameters for widefield data on motion correction

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 5 comments
Labels: type: question

#1168 - Tracking issue: Investigate alternatives to z5py

Issue - State: open - Opened by pgunn over 1 year ago - 1 comment
Labels: type: tracking issue

#1167 - Lazy arrays for CNMF

Pull Request - State: open - Opened by kushalkolar over 1 year ago - 16 comments

#1166 - value error with cnm.estimates.nb_view_components

Issue - State: closed - Opened by nprzrosas over 1 year ago - 4 comments
Labels: type: bug

#1165 - Issue when import the package for demo pipeline

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 32 comments
Labels: type: build/install/tests

#1164 - A bug in play_movie function of estimates.py

Issue - State: open - Opened by wsshen over 1 year ago - 1 comment
Labels: type: bug

#1163 - F-Dff Object Returns NoneType

Issue - State: closed - Opened by CraigScullyClemmons over 1 year ago - 2 comments

#1162 - Analysis inside a region designated by a Binary Mask

Issue - State: open - Opened by ggmirandac over 1 year ago - 2 comments
Labels: type: question

#1157 - gSig and gSiz difference

Issue - State: closed - Opened by ggmirandac over 1 year ago - 1 comment
Labels: type: question

#1152 - Quality assurance method for ROI detection

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 7 comments
Labels: type: question

#1151 - Issue with multiprocessing in VS code interactive window

Issue - State: closed - Opened by JohnStout over 1 year ago - 4 comments
Labels: type: question

#1150 - View components problem

Issue - State: closed - Opened by ggmirandac over 1 year ago - 3 comments
Labels: type: question

#1149 - estimates.nb_view_components [and _3d] throws error in demo notebooks

Issue - State: closed - Opened by noahpettit over 1 year ago - 2 comments
Labels: type: bug

#1146 - Create notebook showing how to work with NWB format

Issue - State: open - Opened by EricThomson over 1 year ago - 4 comments
Labels: type: feature request

#1145 - CNMF-e how to use the same mask on different sessions

Issue - State: open - Opened by annahayoon over 1 year ago - 1 comment
Labels: type: question

#1143 - Can I access temporal component w/o detrending & deconvolving?

Issue - State: closed - Opened by mvagabov over 1 year ago - 2 comments
Labels: type: question

#1142 - CaImAn 2023 Roadmap

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

#1141 - better documentation of serializing CNMF models to disk and loading them in

Issue - State: open - Opened by kushalkolar over 1 year ago - 1 comment
Labels: type: documentation, type: feature request

#1140 - Bokeh Error by defining the notebook_extension

Issue - State: closed - Opened by ggmirandac over 1 year ago - 6 comments
Labels: type: bug

#1139 - Clarify gSiz parameter role(s)

Issue - State: open - Opened by EricThomson over 1 year ago
Labels: type: documentation, good first issue

#1138 - Different result of pipeline and OnACID

Issue - State: closed - Opened by chimmut over 1 year ago - 2 comments

#1137 - Attempt to load avi throws importerror

Issue - State: closed - Opened by EricThomson over 1 year ago - 14 comments
Labels: type: bug

#1136 - reconstruct the movie according to ROIs

Issue - State: open - Opened by zhouyi0812 over 1 year ago - 3 comments
Labels: type: question

#1135 - 'NoneType' object is not subscriptable when running estimates.S

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 11 comments
Labels: type: question

#1134 - OnACID fit_online initialization does not match with minibatch size

Issue - State: closed - Opened by andyrdar over 1 year ago - 3 comments
Labels: type: bug

#1133 - Fix `subidx` to enable computing the NoRMCorre template frame from subset of movie frames

Pull Request - State: open - Opened by ludovicbellier over 1 year ago - 12 comments
Labels: status: under review, type: enhancement

#1132 - Fix flickering movie when using embed_opencv mode

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

#1131 - Create a demo notebook for seeding CNMFE

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

#1130 - Issues with manually seeding CNMF-E

Issue - State: open - Opened by wmsheer over 1 year ago - 10 comments
Labels: type: question

#1129 - updated vis tools to work with new bokeh

Pull Request - State: open - Opened by EricThomson over 1 year ago - 9 comments
Labels: status: in progress

#1128 - Strategies for reducing size/storage - uint8?

Issue - State: closed - Opened by melkalliny over 1 year ago - 17 comments

#1127 - Our bokeh calls rely on flags removed in bokeh 3.x

Issue - State: closed - Opened by pgunn over 1 year ago - 6 comments
Labels: type: bug, upstream

#1126 - Tracking task: Migrate from tensorflow to pytorch (or possibly numba)

Issue - State: open - Opened by pgunn over 1 year ago - 8 comments
Labels: help wanted, type: feature request, type: discussion

#1125 - Update README.md

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

#1124 - Do you guys still have access to the human-labeled ground-truth data from the paper?

Issue - State: closed - Opened by loftusa over 1 year ago - 3 comments
Labels: type: question

#1123 - Phasing out the wiki

Issue - State: open - Opened by EricThomson over 1 year ago
Labels: type: documentation, status: in progress

#1122 - `extract_patch_coordinates` outputs overlapped patches when `stride` is set to 0

Issue - State: closed - Opened by rob-the-bot over 1 year ago - 6 comments
Labels: type: question

#1121 - Can I get a sanity check from you guys?

Issue - State: closed - Opened by loftusa over 1 year ago - 10 comments
Labels: type: question

#1120 - None of the backends could be imported

Issue - State: closed - Opened by zyazdani-92 over 1 year ago - 13 comments
Labels: type: bug

#1119 - Can't load saved results in caiman GUI

Issue - State: closed - Opened by chriski777 over 1 year ago - 4 comments
Labels: type: question

#1118 - fastplotlib demos for caiman notebooks

Issue - State: closed - Opened by kushalkolar over 1 year ago - 3 comments
Labels: type: discussion

#1117 - `display_movie` line dies in remote jupyter kernel

Issue - State: closed - Opened by loftusa over 1 year ago - 2 comments
Labels: type: question

#1116 - Add patch visualization for motion correction and CNMF

Issue - State: closed - Opened by EricThomson over 1 year ago - 2 comments
Labels: type: feature request

#1115 - Package caiman not found

Issue - State: closed - Opened by CatarinaPachec over 1 year ago - 10 comments
Labels: type: build/install/tests

#1114 - Parametrization setup with .TIF

Issue - State: closed - Opened by andyrdar over 1 year ago - 4 comments
Labels: type: question

#1113 - do you guys want plotting code?

Issue - State: closed - Opened by loftusa over 1 year ago - 3 comments
Labels: type: discussion

#1112 - `cnmf_obj.estimates.idx_components` should include all indices if no bad components were found

Issue - State: closed - Opened by loftusa over 1 year ago - 3 comments
Labels: type: question

#1111 - `caimanmanager.py` requires conda

Issue - State: closed - Opened by loftusa over 1 year ago - 4 comments

#1110 - Running the CNMF demo pipeline with p=2 causes the pipeline to hang on my system

Issue - State: open - Opened by loftusa over 1 year ago - 7 comments
Labels: type: question

#1109 - Revert "Change doc theme from classic to alabaster"

Pull Request - State: open - Opened by EricThomson over 1 year ago - 1 comment

#1108 - load background `b` as a sparse matrix, not dict

Issue - State: open - Opened by loftusa over 1 year ago - 5 comments
Labels: type: question

#1107 - Add save/load methods to CNMFParams Class

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

#1106 - Build in motion correction on subset of movie (temporal crop)

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

#1105 - Download high resolution analysis figure

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 11 comments
Labels: type: question

#1104 - Issue with install caimanmanager: No such file or directory after entering the full path

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 4 comments

#1103 - cnmf/online_cnmf.py:OnACID.initialize_online(): Fix call to np.percentile()

Pull Request - State: closed - Opened by pgunn over 1 year ago - 2 comments

#1102 - demo_OnACID_mesoscope CLI demo: show_movie is broken

Issue - State: closed - Opened by pgunn over 1 year ago - 15 comments
Labels: type: bug

#1101 - play movies w/o loading them into memory

Pull Request - State: closed - Opened by j-friedrich over 1 year ago - 10 comments

#1100 - Unable to create file "Tolias_mesoscope_1_results"

Issue - State: closed - Opened by chimmut over 1 year ago - 19 comments
Labels: type: bug

#1099 - spatial comps visualization for ipython notebook

Issue - State: closed - Opened by caichangjia over 1 year ago - 4 comments
Labels: status: under investigation

#1098 - Change doc theme from classic to alabaster

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

#1097 - why it took so long to run CNMF-E in Jupyter notebook

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 10 comments
Labels: type: bug

#1096 - Have the ipynb notebooks in the demos be shown ran

Issue - State: closed - Opened by loftusa over 1 year ago - 6 comments
Labels: type: discussion

#1095 - Issues loading UCLA V4 Miniscope .avi files

Issue - State: closed - Opened by wmsheer over 1 year ago - 15 comments
Labels: type: bug

#1094 - Readme update

Pull Request - State: closed - Opened by EricThomson over 1 year ago - 3 comments
Labels: status: under review

#1093 - Manually changing good and bad component indices

Issue - State: closed - Opened by kushalkolar over 1 year ago - 2 comments
Labels: type: feature request

#1092 - Dendritic/axonal contours

Issue - State: closed - Opened by vkonan over 1 year ago - 10 comments
Labels: type: question

#1091 - unable to upload the .tif

Issue - State: closed - Opened by zhouyi0812 over 1 year ago - 5 comments
Labels: type: bug

#1090 - Tracking task: Build issue in conda-forge on OSX/Intel

Issue - State: closed - Opened by pgunn over 1 year ago - 3 comments

#1089 - tensorflow corrupted error when first installing CaImAn

Issue - State: closed - Opened by ziyizhu1996 over 1 year ago - 3 comments

#1088 - estimates.center is None in demo pipeline

Issue - State: open - Opened by EricThomson over 1 year ago
Labels: good first issue

#1087 - Bridge to Pynapple

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

#1086 - Save final results to csv and other formats

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

#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

GitHub / flatironinstitute/CaImAn issues and pull requests