Ecosyste.ms: Issues

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

GitHub / microscopium/microscopium issues and pull requests

#180 - Downloading Images

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

#178 - Don't update settings in-place when removing default key

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

#177 - "500 Internal Error"

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

#176 - Failing test due to h5py

Issue - State: open - Opened by jni about 4 years ago
Labels: bug

#175 - Update bokeh =>2.0.0

Pull Request - State: closed - Opened by GenevieveBuckley about 4 years ago - 5 comments

#174 - Pin bokeh to =>1.0.0 and <2.0.0

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

#173 - Error 500 on demo after install bokeh 2.2.3

Issue - State: closed - Opened by Gpotier about 4 years ago - 1 comment

#172 - TEST: Move from Travis to Github Actions for testing

Issue - State: open - Opened by GenevieveBuckley over 4 years ago - 1 comment

#171 - Consider star clustering for validation

Issue - State: open - Opened by GenevieveBuckley over 4 years ago - 1 comment

#170 - Refreshing the web page causes the app to crash

Issue - State: open - Opened by GenevieveBuckley over 5 years ago - 1 comment

#169 - Replace image_rgba calls with image_url

Pull Request - State: closed - Opened by jni over 5 years ago - 3 comments

#168 - Update serve.py to respect --url arg

Pull Request - State: closed - Opened by GenevieveBuckley over 5 years ago - 1 comment

#167 - New features enabled by Bokeh 1.3

Issue - State: open - Opened by jni over 5 years ago

#166 - Print web app url in the terminal when the bokeh server is launched

Pull Request - State: closed - Opened by GenevieveBuckley over 5 years ago - 1 comment

#165 - Remove all mongo related files

Pull Request - State: closed - Opened by GenevieveBuckley over 5 years ago - 1 comment

#164 - Actually use glpyh_size from the user provided config

Pull Request - State: closed - Opened by GenevieveBuckley over 5 years ago - 2 comments

#160 - Update README.md

Pull Request - State: closed - Opened by GenevieveBuckley over 5 years ago - 1 comment

#159 - config.yml - recursive formatting all numeric values to float

Issue - State: closed - Opened by GenevieveBuckley over 5 years ago - 8 comments

#158 - Replace arbitrary categories by geneID

Pull Request - State: closed - Opened by jni over 5 years ago - 1 comment

#157 - Remove mongo

Pull Request - State: closed - Opened by jni over 5 years ago - 1 comment

#156 - Possible simplification for make_makedoc

Issue - State: open - Opened by jni over 5 years ago

#155 - Investigate jupyter itk-widgets for multi-volume rendering

Issue - State: open - Opened by GenevieveBuckley over 5 years ago - 4 comments

#153 - Clean up old mongo code

Issue - State: closed - Opened by jni over 5 years ago - 1 comment

#151 - Better navigation of images

Issue - State: open - Opened by jni over 5 years ago - 1 comment

#150 - Support more pre-filtering at the outset

Issue - State: open - Opened by jni over 5 years ago - 3 comments

#149 - Add ability to "permanently" remove images from plot

Issue - State: open - Opened by jni over 5 years ago

#148 - Export feature signatures for selected cluster

Issue - State: open - Opened by jni over 5 years ago - 5 comments

#147 - Add a master configuration file for start-to-finish processing

Pull Request - State: open - Opened by jni over 5 years ago - 1 comment

#146 - Add input.csv file for pipeline testing

Pull Request - State: closed - Opened by GenevieveBuckley over 5 years ago - 1 comment

#145 - Audit code for possible improvements with Bokeh 1.2

Issue - State: open - Opened by jni over 5 years ago

#144 - Haralick texture features

Pull Request - State: closed - Opened by GenevieveBuckley over 5 years ago - 6 comments

#143 - Pipelines feature

Issue - State: open - Opened by GenevieveBuckley over 5 years ago

#141 - Generalized feature computation function

Issue - State: open - Opened by GenevieveBuckley over 5 years ago

#139 - Update config.py to use yaml.safe_load()

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

#138 - Use yaml.safe_load() or yaml.full_load() to remove deprecation warning

Issue - State: closed - Opened by GenevieveBuckley almost 6 years ago - 1 comment

#137 - Improve settings handling

Pull Request - State: closed - Opened by jni about 6 years ago - 3 comments

#136 - KeyError: 'url' when trying to run

Issue - State: closed - Opened by lucyleeow about 6 years ago - 2 comments

#135 - bokeh.server.protocol_handler error with testdata

Issue - State: closed - Opened by lucyleeow about 6 years ago

#134 - Include default settings file

Issue - State: open - Opened by GenevieveBuckley about 6 years ago

#131 - Potentially useful papers list

Issue - State: open - Opened by jni about 6 years ago - 3 comments

#130 - Reset figure axes (and zoom level) whenever new images are selected.

Pull Request - State: closed - Opened by GenevieveBuckley about 6 years ago - 3 comments

#129 - Add Haralick features

Issue - State: closed - Opened by jni about 6 years ago - 2 comments

#128 - Computing distance values

Issue - State: open - Opened by jni about 6 years ago

#127 - Document basic csv format for input to microscopium.serve

Issue - State: open - Opened by jni about 6 years ago

#126 - Improve help message to show defaults for various values

Issue - State: open - Opened by jni about 6 years ago

#125 - Allow selection of single channel images in image view

Issue - State: open - Opened by jni about 6 years ago

#124 - Reset image view when changing selection

Issue - State: closed - Opened by jni about 6 years ago - 5 comments

#123 - Minor fixes

Pull Request - State: closed - Opened by jni about 6 years ago - 3 comments

#122 - Fast switching between pan and box select modes in the bokeh web app

Issue - State: open - Opened by GenevieveBuckley about 6 years ago
Labels: enhancement

#121 - Hover tool for selected images plot

Issue - State: open - Opened by GenevieveBuckley about 6 years ago - 2 comments
Labels: enhancement

#119 - DOC: readme now states supported browsers are Chrome and Firefox

Pull Request - State: closed - Opened by GenevieveBuckley about 6 years ago - 1 comment

#118 - Update environment.yml, must have bokeh>=1.0.0

Pull Request - State: closed - Opened by GenevieveBuckley about 6 years ago - 2 comments

#117 - Make legend slightly transparent.

Pull Request - State: closed - Opened by GenevieveBuckley about 6 years ago - 1 comment

#115 - Use coordinates='rc' when calling regionprops

Pull Request - State: closed - Opened by jni about 6 years ago - 1 comment

#114 - Update montaging with missing files

Pull Request - State: closed - Opened by jni over 6 years ago - 3 comments

#113 - Missing channel stitching

Pull Request - State: closed - Opened by jni over 6 years ago - 1 comment

#112 - Automatically determine stitching pattern from list of images

Issue - State: open - Opened by jni over 6 years ago

#111 - Download table feature doesn't work on Safari (Mac OS)

Issue - State: closed - Opened by GenevieveBuckley over 6 years ago - 1 comment

#110 - Bokeh app command line argument --color-column cannot handle numeric data

Issue - State: closed - Opened by GenevieveBuckley over 6 years ago - 2 comments
Labels: bug

#109 - Add tests for web app using Selenium

Issue - State: open - Opened by GenevieveBuckley over 6 years ago - 4 comments

#108 - Upgrade to bokeh 1.0.0

Pull Request - State: closed - Opened by GenevieveBuckley over 6 years ago - 2 comments

#107 - FEATURE REQUEST: filter datapoints by z-factor (or overlay z-factor information)

Issue - State: open - Opened by GenevieveBuckley over 6 years ago
Labels: enhancement

#106 - Large images and gifs

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

#105 - Update readme

Pull Request - State: closed - Opened by GenevieveBuckley over 6 years ago - 3 comments

#104 - Set wheel zoom as the active scroll tool on scatterplot

Pull Request - State: closed - Opened by jni over 6 years ago - 1 comment

#103 - [WIP] FEAT: Support for 3d image data

Pull Request - State: open - Opened by GenevieveBuckley over 6 years ago - 1 comment

#102 - Wheel zoom should be on by default for bokeh scatterplot figure

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

#101 - Update requirements

Pull Request - State: closed - Opened by GenevieveBuckley over 6 years ago - 4 comments

#100 - Consider using colorblind friendly channel colours

Issue - State: open - Opened by jni over 6 years ago - 2 comments

#99 - Dropdown menu to switch scatterplot colourmap according to different columns

Issue - State: open - Opened by GenevieveBuckley over 6 years ago - 4 comments
Labels: enhancement

#98 - Clickable image plot to open volume rendering html

Issue - State: open - Opened by GenevieveBuckley over 6 years ago
Labels: enhancement

#97 - Custom logo for microscopium

Issue - State: open - Opened by GenevieveBuckley over 6 years ago - 2 comments

#96 - Make legend slightly transparent on scatterplot

Issue - State: closed - Opened by GenevieveBuckley over 6 years ago - 1 comment
Labels: enhancement

#94 - Force delay before opening volume rendered html in new tab

Issue - State: open - Opened by GenevieveBuckley over 6 years ago - 1 comment
Labels: bug

#93 - Add button group to toggle between plot data sources

Pull Request - State: closed - Opened by jamesryan094 over 6 years ago - 10 comments

#91 - Update bokeh gallery examples with our new and improved versions

Issue - State: open - Opened by jni over 6 years ago - 4 comments

#89 - Javascript error when updating table display (PR #87 export-data)

Issue - State: closed - Opened by GenevieveBuckley over 6 years ago - 12 comments
Labels: bug

#87 - [FEAT] microscopium user interface, export selected data

Pull Request - State: closed - Opened by GenevieveBuckley over 6 years ago - 8 comments

#73 - Bokeh prototype

Issue - State: closed - Opened by birdsarah over 8 years ago - 18 comments

#56 - Profile and speed up global illumination correction

Issue - State: closed - Opened by jni over 9 years ago - 1 comment

#53 - Figure out mongo sample _id

Issue - State: closed - Opened by jni over 9 years ago - 4 comments

#51 - add parser for VCFG screen request form

Issue - State: closed - Opened by jni over 9 years ago - 1 comment

#49 - Create conda files

Issue - State: closed - Opened by jni almost 10 years ago

#47 - Add fully-automated/unbiased feature detectors

Issue - State: open - Opened by jni almost 10 years ago - 6 comments

#42 - Add configurable "treatment" field to Mongo schema

Issue - State: closed - Opened by jni almost 10 years ago - 1 comment

#41 - Add command-line interface to build mongoDB for a new screen

Issue - State: closed - Opened by jni almost 10 years ago - 2 comments

#39 - Make a full run of the Myores dataset

Issue - State: closed - Opened by jni almost 10 years ago