Ecosyste.ms: Issues

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

GitHub / MPI-Dortmund/tomotwin-cryoet issues and pull requests

#106 - Making turning a segmentation into a binary mask

Issue - State: open - Opened by hamid13r about 2 months ago

#105 - Update torchtrainer.py

Pull Request - State: open - Opened by YousefMetwally 4 months ago

#104 - Update installation.rst

Pull Request - State: closed - Opened by YousefMetwally 4 months ago - 1 comment

#103 - Single forward run for embedding of anchor, negative and positive volumes.

Pull Request - State: closed - Opened by YousefMetwally 4 months ago - 1 comment

#102 - Auto encoder

Pull Request - State: closed - Opened by YousefMetwally 4 months ago

#101 - environment creation command in docs doesn't work

Issue - State: closed - Opened by alisterburt 5 months ago - 3 comments

#100 - Issue with environment creation

Issue - State: open - Opened by alisterburt 5 months ago - 1 comment

#99 - Update installation.rst

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

#98 - Update changes link

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

#97 - Update to napari 0.4.19

Issue - State: open - Opened by thorstenwagner 7 months ago
Labels: maintenance

#96 - Switch to SPDX-License-Identifiers

Pull Request - State: closed - Opened by kephale 7 months ago - 1 comment

#95 - Adjusting license headers

Issue - State: closed - Opened by kephale 7 months ago - 2 comments

#94 - Update documentation to cover new napari-tomotwin features

Issue - State: open - Opened by thorstenwagner 8 months ago
Labels: documentation

#93 - Reduce number of forward passes during training for speed-up

Issue - State: open - Opened by thorstenwagner 8 months ago
Labels: enhancement, good first issue

#92 - Use dask to speed-up the locate command

Issue - State: closed - Opened by thorstenwagner 8 months ago
Labels: enhancement

#91 - Remove tomotwin from env file

Pull Request - State: closed - Opened by thorstenwagner 8 months ago

#90 - Locate is now using dask

Pull Request - State: closed - Opened by thorstenwagner 8 months ago - 1 comment

#89 - Fast locate, new rapdis and updated tutorial

Pull Request - State: closed - Opened by thorstenwagner 8 months ago - 2 comments

#88 - Update to Rapids 23.12

Issue - State: closed - Opened by thorstenwagner 8 months ago
Labels: maintenance

#87 - Update pytorch-metric-learning

Pull Request - State: closed - Opened by thorstenwagner 10 months ago - 1 comment

#86 - Label mask is not specificed

Issue - State: open - Opened by DrJesseHansen 10 months ago - 11 comments

#85 - UMAP manifold error

Issue - State: closed - Opened by ffigueiredo85 10 months ago - 13 comments

#84 - Release v0.8.0

Pull Request - State: closed - Opened by thorstenwagner 10 months ago - 2 comments

#83 - About Model Training and Loss Function

Issue - State: open - Opened by JachyLikeCoding 10 months ago - 2 comments

#81 - add short training tutorial

Pull Request - State: closed - Opened by thorstenwagner 10 months ago - 1 comment

#80 - Inquiry Regarding Model Training and Resource Requirements

Issue - State: closed - Opened by JachyLikeCoding 10 months ago - 2 comments

#79 - fix numbering

Pull Request - State: closed - Opened by GavinR1 11 months ago

#78 - Stop making tomotwin_tools crash on non gpu machines.

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#77 - TomoTwin_tools loads all tool dependencies

Issue - State: closed - Opened by GavinR1 11 months ago - 1 comment

#76 - Add median filter strategy

Pull Request - State: closed - Opened by GavinR1 11 months ago - 2 comments

#75 - napari_boxmanager by x-windows

Issue - State: closed - Opened by kimdn 11 months ago - 2 comments

#74 - CUDA/torch error since updating to 0.7.0

Issue - State: closed - Opened by rdrighetto 11 months ago - 10 comments

#73 - Install tomotwin by mamba

Issue - State: closed - Opened by kimdn 11 months ago - 3 comments

#72 - Check if ldconfig is in path

Issue - State: open - Opened by thorstenwagner 11 months ago
Labels: enhancement

#71 - add links to strategies

Pull Request - State: closed - Opened by thorstenwagner 11 months ago

#70 - Adds an images to strategies

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#69 - Link strategies in tutorial

Pull Request - State: closed - Opened by thorstenwagner 11 months ago

#68 - make headlines

Pull Request - State: closed - Opened by thorstenwagner 11 months ago

#67 - This PR adds strategies to the documentation

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#66 - Add fast median mask estimation

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#65 - Fix padding when creating heatmaps during locate with `--write_heatmaps`

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#64 - Add new umap and filter options

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#63 - Add connected components picking as alternative to findmax

Issue - State: open - Opened by thorstenwagner 11 months ago
Labels: enhancement

#62 - Use distributed umap from rapids

Issue - State: open - Opened by thorstenwagner 11 months ago
Labels: enhancement

#61 - Check & correct for duplicate embedded subvolumes

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#60 - `--save_after_improvement` saves models after each epoch

Pull Request - State: closed - Opened by thorstenwagner 11 months ago - 1 comment

#59 - boxmanager doesn't open

Issue - State: closed - Opened by azazellochg 11 months ago - 7 comments

#58 - v0.6.1 mask creation fails

Issue - State: closed - Opened by azazellochg 11 months ago - 23 comments

#57 - increase timeout of the dataloader to 180 seconds.

Pull Request - State: closed - Opened by thorstenwagner 12 months ago - 1 comment

#56 - Fix 'too many open files' problem

Pull Request - State: closed - Opened by thorstenwagner 12 months ago - 1 comment

#55 - Fix read the docs building

Pull Request - State: closed - Opened by thorstenwagner 12 months ago - 1 comment

#54 - Use random port for distributed processing

Pull Request - State: closed - Opened by thorstenwagner 12 months ago - 1 comment

#53 - memory issue of tomotwin_locate.py

Issue - State: closed - Opened by jychoi0616 12 months ago - 11 comments

#52 - Use stable pytorch 2.1

Pull Request - State: closed - Opened by thorstenwagner 12 months ago

#51 - pytorch related warning/errors

Issue - State: closed - Opened by jychoi0616 12 months ago - 8 comments

#50 - Fix version youtube contrib package

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

#49 - Update version of latest model

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

#48 - Update rapids to 23.10

Pull Request - State: closed - Opened by thorstenwagner about 1 year ago - 3 comments

#47 - Update checks_tests_deploy.yml

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

#46 - Unpin pytorch

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

#45 - Update to rapids 23.10

Issue - State: closed - Opened by thorstenwagner about 1 year ago
Labels: maintenance

#44 - Update to latest metric-learning library

Issue - State: closed - Opened by thorstenwagner about 1 year ago
Labels: maintenance

#43 - unpin metric learning lib

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

#42 - libcublas.so.11 error

Issue - State: closed - Opened by jychoi0616 about 1 year ago - 3 comments

#41 - note on installation: non-GPU pytorch installed

Issue - State: closed - Opened by nitishnih about 1 year ago - 1 comment

#40 - Speed up TomoTwin: Use pytorch 2 and DistributedDataParallel

Pull Request - State: closed - Opened by thorstenwagner about 1 year ago - 4 comments

#39 - update installation instructions

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

#38 - Installation instructions updt

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

#37 - Interactive clustering crashes with napari 0.4.18

Issue - State: open - Opened by thorstenwagner about 1 year ago
Labels: bug

#36 - use napari 0.4.17 for now

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

#35 - Add update instructions

Issue - State: closed - Opened by thorstenwagner about 1 year ago - 1 comment
Labels: documentation

#34 - Updated documentation

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

#33 - fix labeling bug

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

#31 - fix typo

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

#30 - fix typos

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

#29 - Update docs to fix some typos

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

#28 - update documentation for masking

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

#27 - Add option to specify a mask during embedding

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

#26 - Added some developer information and slightly updated documentation

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

#25 - Merge clusters

Issue - State: open - Opened by thorstenwagner over 1 year ago - 1 comment
Labels: enhancement

#24 - Embedding ROI specification by binary mask

Issue - State: closed - Opened by thorstenwagner over 1 year ago - 4 comments
Labels: enhancement

#23 - Editing readthedocs

Pull Request - State: closed - Opened by GavinR1 over 1 year ago - 2 comments

#22 - Add citation nmeth to index and citation.cff

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

#21 - Updated dependencies and new installation instructions

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

#20 - TomoTwin installation issues

Issue - State: closed - Opened by bionanopatterning over 1 year ago - 7 comments
Labels: bug

#19 - Auto release

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

#18 - Add the citation.cff

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

#17 - remove "follow soon" sentence :-)

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

#16 - add YT video to clustering tutorial

Pull Request - State: closed - Opened by GavinR1 over 1 year ago - 2 comments

#14 - correct typo

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

#13 - update installation instructions

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

#12 - add changes for 0.4.0

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

#11 - Clustering workflow release

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

#10 - Added more unit tests, documentation and did some refactoring

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

#9 - Refactor locate and add unit tests

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

#8 - Make pytest and coverage running

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

#7 - Move to pyTorch 2.x

Issue - State: closed - Opened by thorstenwagner over 1 year ago - 1 comment
Labels: enhancement

#6 - import error

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