Ecosyste.ms: Issues

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GitHub / BBQuercus/deepBlink issues and pull requests

#151 - Benchmark of DetNet and spotlearn

Issue - State: closed - Opened by wikk-chy over 1 year ago - 2 comments
Labels: bug

#150 - CPU / GPU configuration - 3D spot detection jupyter notebook

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

#146 - deepblink model

Issue - State: closed - Opened by wikk-chy about 2 years ago - 6 comments
Labels: bug

#145 - Prepare for release 0.1.4

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

#144 - TrackMate output file changes

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

#143 - Comparison between deepBlink and spotlearn

Issue - State: closed - Opened by imzhangyd over 2 years ago - 1 comment
Labels: enhancement

#142 - tiff images not allowed in predict

Issue - State: closed - Opened by SosUts over 2 years ago - 2 comments
Labels: bug

#141 - Intensity and radius bug

Pull Request - State: closed - Opened by BBQuercus almost 3 years ago - 1 comment

#140 - Error when using both probability and radius parameters

Issue - State: closed - Opened by nickeener almost 3 years ago - 3 comments
Labels: bug

#139 - Release 0.1.3

Pull Request - State: closed - Opened by BBQuercus almost 3 years ago - 1 comment

#137 - What's the training data of your pretrained model?

Issue - State: closed - Opened by imzhangyd almost 3 years ago - 4 comments

#136 - Scale pixel size predict

Pull Request - State: closed - Opened by BBQuercus almost 3 years ago - 1 comment

#135 - Scale pixel size in deepblink create

Pull Request - State: closed - Opened by BBQuercus almost 3 years ago - 1 comment

#134 - CLI submodule visualize

Pull Request - State: closed - Opened by BBQuercus almost 3 years ago - 1 comment

#133 - How to fine-tune with my custom data?

Issue - State: closed - Opened by tamasbalassa almost 3 years ago - 16 comments
Labels: enhancement

#132 - Release 0.1.2

Pull Request - State: closed - Opened by BBQuercus about 3 years ago - 1 comment

#131 - New models and trackmate version support

Pull Request - State: closed - Opened by BBQuercus over 3 years ago - 1 comment
Labels: bug, enhancement

#130 - [training data loading] to adapte csvs exported from Trackmate v7.0.0+

Pull Request - State: closed - Opened by BioinfoTongLI over 3 years ago - 3 comments

#129 - Optimization for large images?

Issue - State: closed - Opened by BioinfoTongLI over 3 years ago - 5 comments
Labels: enhancement

#128 - Create QOL

Pull Request - State: closed - Opened by BBQuercus over 3 years ago - 1 comment

#127 - Pre training

Pull Request - State: closed - Opened by BBQuercus over 3 years ago - 1 comment

#126 - Fix bugs in 3d prediction notebook example

Pull Request - State: closed - Opened by zhanyinx over 3 years ago - 1 comment

#125 - Creation of npz dataset file fails

Issue - State: closed - Opened by mimuelle almost 4 years ago - 2 comments
Labels: bug

#124 - Add 3D prediction example notebook

Pull Request - State: closed - Opened by BBQuercus almost 4 years ago - 1 comment

#123 - Reminder: No test data.

Issue - State: closed - Opened by BBQuercus almost 4 years ago - 1 comment
Labels: enhancement

#122 - Example notebooks

Pull Request - State: closed - Opened by BBQuercus almost 4 years ago - 1 comment

#121 - Timeout and intensity

Pull Request - State: closed - Opened by BBQuercus almost 4 years ago - 1 comment

#120 - Calling deepblink from jupyter notebook

Issue - State: closed - Opened by mimuelle almost 4 years ago - 3 comments
Labels: enhancement

#119 - Prediction output

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#118 - prediction probability in the output

Issue - State: closed - Opened by alcrevenna about 4 years ago - 8 comments
Labels: enhancement

#117 - Prediction of non-square images

Issue - State: closed - Opened by BBQuercus about 4 years ago
Labels: bug

#116 - Add twitter and PyPI downloads in README

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#115 - Add citation to README!

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#114 - Release 0.1!

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#112 - Bumpversion, new images, bugfix

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#111 - Raw configuration

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#110 - Add gaussian localization benchmark

Pull Request - State: closed - Opened by zhanyinx about 4 years ago - 1 comment

#109 - Network bugs

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#108 - Pre release 0.1.0 / Patch 0.0.7

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#107 - ValueError: Unknown activation function:leaky_relu

Issue - State: closed - Opened by resace3 about 4 years ago - 9 comments
Labels: bug

#106 - Add models.txt for deepBlink download

Pull Request - State: closed - Opened by BBQuercus about 4 years ago - 1 comment

#105 - Final adjustments

Pull Request - State: closed - Opened by zhanyinx about 4 years ago - 1 comment

#104 - Final inception architecture

Pull Request - State: closed - Opened by zhanyinx about 4 years ago - 1 comment

#103 - Qol improvements

Pull Request - State: closed - Opened by zhanyinx over 4 years ago - 1 comment

#102 - 📰 Add TrackMate labelling image

Pull Request - State: closed - Opened by BBQuercus over 4 years ago - 1 comment

#101 - Small fixes

Pull Request - State: closed - Opened by zhanyinx over 4 years ago - 1 comment

#100 - Move train argument description to yaml config

Pull Request - State: closed - Opened by zhanyinx over 4 years ago - 1 comment

#99 - Wandb logging

Pull Request - State: closed - Opened by BBQuercus over 4 years ago - 1 comment

#98 - ⬆️ Bump tensorflow from 2.2.0 to 2.2.1

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#97 - Improve test coverage

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

#96 - Benchmarks add run scripts

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

#95 - Add more descriptive help text messages

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

#94 - Cli create image cropping

Pull Request - State: closed - Opened by BBQuercus over 4 years ago - 1 comment

#93 - Cli helptext

Pull Request - State: closed - Opened by BBQuercus over 4 years ago - 1 comment

#92 - Update CI system

Pull Request - State: closed - Opened by BBQuercus over 4 years ago - 1 comment

#91 - Add license scan report and status

Pull Request - State: closed - Opened by fossabot over 4 years ago - 1 comment

#90 - Make the CLI great again

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#89 - Cli create submodule

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#88 - Cli config submodule

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#87 - Channel option in cli

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#86 - Docs update

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#85 - Cli ndimensional prediction

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#84 - Match tensorflow's dependencies

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#83 - Cli redesign to contain submodules

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#82 - Release 0.0.6

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#81 - Cli intensity calculation

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#80 - Cleanup resnet, implementation of inception block

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#79 - Remove pre-commit

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#78 - Cli bce rmse

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#77 - It's benchmarking time

Pull Request - State: closed - Opened by BBQuercus over 4 years ago
Labels: enhancement

#76 - F1 bug and wandb naming

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#75 - Add configurable fcn

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#74 - Fix losses output shapes

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#73 - Load npz bug fix

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#72 - Add combined_bce_rmse loss function

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#71 - `test_only` searching for all components.

Issue - State: closed - Opened by BBQuercus over 4 years ago
Labels: bug

#70 - Doi and modules

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#68 - Add new features in network args for network sparseness

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#67 - Quality of life; load_npz training only; overfit flag

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#66 - Addition of benchmarking(s)

Issue - State: closed - Opened by BBQuercus over 4 years ago - 1 comment
Labels: enhancement

#65 - XY coordinate format to RC change

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#64 - Add cell_size to resnet architecture

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#63 - Preparation for release 0.0.5

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#62 - Documentation improvement for usage

Issue - State: closed - Opened by BBQuercus over 4 years ago
Labels: enhancement

#61 - XY to RC conversion

Issue - State: closed - Opened by BBQuercus over 4 years ago - 1 comment
Labels: enhancement

#60 - Convert prediction matrix dataset into coordinates

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#59 - Convert prediction matrix dataset into coordinates

Issue - State: closed - Opened by BBQuercus over 4 years ago - 2 comments
Labels: enhancement

#58 - Unittest improvements; rename get_abs to abs

Pull Request - State: closed - Opened by BBQuercus over 4 years ago

#57 - Increase test suite

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#56 - Test initialization

Pull Request - State: closed - Opened by zhanyinx over 4 years ago

#55 - Functional reordering

Pull Request - State: closed - Opened by BBQuercus over 4 years ago
Labels: enhancement

#54 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by BBQuercus over 4 years ago - 1 comment

#53 - Adoption of new F1 calculation

Pull Request - State: closed - Opened by BBQuercus over 4 years ago
Labels: enhancement

#52 - Update numpy to 1.19.1

Pull Request - State: closed - Opened by pyup-bot over 4 years ago

#51 - Update tensorflow to 2.3.0

Pull Request - State: closed - Opened by pyup-bot over 4 years ago

#49 - Update tox to 3.19.0

Pull Request - State: closed - Opened by pyup-bot over 4 years ago

#46 - Update tensorflow to 2.3.0

Pull Request - State: closed - Opened by pyup-bot over 4 years ago

#45 - Update wandb to 0.9.4

Pull Request - State: closed - Opened by pyup-bot over 4 years ago

#44 - Update scipy to 1.5.2

Pull Request - State: closed - Opened by pyup-bot over 4 years ago