juglab/cryoCARE_pip issues and pull requests

#61 - tensorflow-2.4 vs tensorflow-2.5 ?

Issue - State: open - Opened by EricDeveaud 2 months ago

#60 - Update README.md :

Pull Request - State: closed - Opened by TomCrey 3 months ago - 16 comments

#59 - Change the output name to something independent from odd/even?

Issue - State: open - Opened by rdrighetto 3 months ago - 3 comments

#58 - Fixed bug in mask-parser

Pull Request - State: closed - Opened by bwmr 5 months ago

#57 - listing more than one tomograms

Issue - State: closed - Opened by jychoi0616 7 months ago

#56 - Dependency conflicts

Issue - State: open - Opened by JadisInka 7 months ago

#55 - Implementation of Masked Extraction (Issue #54)

Pull Request - State: closed - Opened by bwmr 7 months ago

#54 - Extract only in sample volume?

Issue - State: closed - Opened by bwmr 7 months ago - 1 comment

#53 - F tensorflow/stream_executor/cuda/cuda_dnn.cc:88] Check failed: narrow == wide (-2128347136 vs. 2166620160)checked narrowing failed; values not equal post-conversion

Issue - State: closed - Opened by rnwokonko 8 months ago - 4 comments

#52 - Artifact in denoised tomogram?

Issue - State: open - Opened by asarnow 11 months ago - 1 comment

#51 - GPU usage

Issue - State: closed - Opened by JulienMaufront about 1 year ago - 4 comments

#50 - documentation?

Issue - State: open - Opened by McHaillet about 1 year ago - 1 comment

#49 - set numpy version compatible with 1.19.2 to fix installation issue

Pull Request - State: closed - Opened by McHaillet about 1 year ago - 1 comment

#48 - json.decoder.JSONDecodeError: Expecting value: line 12 column 16 (char 320)

Issue - State: open - Opened by CleoShen about 1 year ago - 1 comment

#47 - numpy versions in conflict.... tensorflow vs cryoCARE

Issue - State: closed - Opened by pconesa about 1 year ago - 5 comments

#46 - Unusual index error in cryoCARE_extract_training_data.py

Issue - State: open - Opened by jmdobbs over 1 year ago - 1 comment

#45 - pinned to TF2.4

Issue - State: open - Opened by alisterburt over 1 year ago - 1 comment

#44 - copy extended header into output file

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

#43 - Failing to read tomograms written out by cryoCARE

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

#42 - np.bool is depreciated in latest numpy version, this prevents error

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

#41 - Fixing predict json

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

#40 - cryoCARE_predict.py unable to run (cryocare_11)

Issue - State: closed - Opened by virlyananda over 1 year ago - 10 comments

#39 - potential fix to issue 38

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

#38 - Latest version leads to crash during random coordinate sampling

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

#37 - Prediction step error

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

#36 - assert even.data.shape[0] > 2 * sample_shape[0] error

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

#35 - Distributed implementation using mirrored strategy

Pull Request - State: closed - Opened by rdrighetto over 1 year ago - 9 comments

#34 - Fixes in augment() and in validation dataset generation

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

#33 - Fix quality issues

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

#32 - White density around the denoised membrane

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

#31 - mrc data mode?

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

#30 - Results from cryoCARE_pip looking worse than cryoCARE_T2T

Issue - State: closed - Opened by rdrighetto almost 2 years ago - 16 comments

#29 - incorrectly stitched denoised tomogram.mrc

Issue - State: open - Opened by jychoi0616 almost 2 years ago - 15 comments

#28 - Update sample jsons and README

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

#27 - installation issue?

Issue - State: open - Opened by jychoi0616 almost 2 years ago - 4 comments

#26 - using tomogram generated by AreTomo

Issue - State: open - Opened by jychoi0616 almost 2 years ago - 3 comments

#25 - Not running with GPU

Issue - State: open - Opened by YunjieChang almost 2 years ago - 2 comments

#24 - Added GPU ID selection capability

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

#23 - Feature Request: GPU ID selection flag for training and prediction

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

#22 - closed issue #14

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

#21 - Illegal instruction (core dumped) error during preparation step

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

#20 - n_tiles not automatically increased

Issue - State: open - Opened by rdrighetto almost 2 years ago - 6 comments

#19 - Fix for issue #16

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

#18 - Merge MPI Dortmund version into this main repository

Pull Request - State: closed - Opened by thorstenwagner almost 2 years ago - 29 comments

#17 - Merge cryoCARE_mpido into this main repo

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

#16 - n_tiles [1,1,1] produces black volume

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

#15 - Training ERROR (train_config.json)

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

#14 - Training step error

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

#13 - AttributeError: 'DatasetV1Adapter' object has no attribute 'element_spec'

Issue - State: closed - Opened by mcianfrocco about 2 years ago - 13 comments

#12 - cryoCARE_predict.py Check error on V100 and A100 GPUs

Issue - State: closed - Opened by rahelwoldeyes over 2 years ago - 8 comments

#11 - parallelization over multiple GPUs

Issue - State: open - Opened by jychoi0616 over 2 years ago - 7 comments

#10 - Update installation instructions to use keras-gpu

Pull Request - State: closed - Opened by thorstenwagner over 2 years ago

#9 - Fix typo

Pull Request - State: closed - Opened by thorstenwagner over 2 years ago

#8 - Create path before saving training data to disk

Pull Request - State: closed - Opened by thorstenwagner over 2 years ago - 4 comments

#7 - Fix computation for val_cut_off

Pull Request - State: closed - Opened by thorstenwagner over 2 years ago

#6 - can i use this implementation to denoise stacks?

Issue - State: closed - Opened by n1kt0 over 2 years ago - 3 comments

#5 - Clarify path variable ( #4 )

Pull Request - State: closed - Opened by thorstenwagner over 2 years ago - 1 comment

#4 - path variable has to be the same for preparation, training and prediction

Issue - State: closed - Opened by thorstenwagner over 2 years ago

#3 - Update installation instructions to solve issue #2

Pull Request - State: closed - Opened by thorstenwagner over 2 years ago - 1 comment

#2 - Installation instructions are not working

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

#1 - Dataloader

Pull Request - State: closed - Opened by tibuch about 3 years ago

GitHub / juglab/cryoCARE_pip issues and pull requests