qupath/qupath issues and pull requests

#100 - Run Qupath on server

Issue - State: closed - Opened by muntesco about 7 years ago - 2 comments
Labels: question (please use image.sc!)

#99 - identifying Renal Cortex, Medulla and extrarenal tissue.

Issue - State: closed - Opened by khalifa1989 about 7 years ago - 2 comments
Labels: question (please use image.sc!)

#98 - Identifying dye combinations per cell

Issue - State: closed - Opened by slarmour16 about 7 years ago - 5 comments
Labels: question (please use image.sc!)

#97 - How to export PNGs using the batch File/Export TMA data command?

Issue - State: closed - Opened by rawatenator about 7 years ago - 11 comments
Labels: question (please use image.sc!)

#96 - TMA grid view does not show all TMA cores

Issue - State: closed - Opened by DavidMHaumann about 7 years ago - 4 comments
Labels: bug

#95 - How to save coordinates of all points comprising the annotated region

Issue - State: closed - Opened by andanis about 7 years ago - 21 comments
Labels: question (please use image.sc!)

#94 - Running Quopath from command line

Issue - State: closed - Opened by lmiroslaw about 7 years ago - 1 comment
Labels: question (please use image.sc!)

#93 - added option to apply to another channel other than 1

Pull Request - State: closed - Opened by tp81 about 7 years ago - 7 comments

#92 - Saving image in jpeg/tiff/png format

Issue - State: closed - Opened by andanis about 7 years ago - 1 comment
Labels: question (please use image.sc!)

#91 - Set ImageJ plugins directory - failing

Issue - State: closed - Opened by JoaoSantinha about 7 years ago - 3 comments
Labels: bug

#90 - Enter coordinates for ROI rectangle and file name to run cell detection from command line

Issue - State: closed - Opened by aditsanghvi94 about 7 years ago - 1 comment

#89 - tile classifications to annotations - are devided by edges of large tiles

Issue - State: closed - Opened by DavidMHaumann about 7 years ago - 1 comment
Labels: question (please use image.sc!)

#88 - Numerous artefacts in case of "Tile classifications to annotations"

Issue - State: closed - Opened by DavidMHaumann about 7 years ago - 2 comments

#87 - Compilation error on Eclipse

Issue - State: closed - Opened by apurwamishra about 7 years ago - 2 comments

#86 - select annotation results in annotation measurement table causes system crash - bug

Issue - State: closed - Opened by DavidMHaumann about 7 years ago - 4 comments
Labels: duplicate

#85 - TMA dearraying

Issue - State: closed - Opened by tinalegre about 7 years ago - 4 comments
Labels: question (please use image.sc!)

#84 - Compile source under windows

Issue - State: closed - Opened by erexhepa about 7 years ago - 12 comments
Labels: question (please use image.sc!)

#83 - How to detect nuclei with different staining

Issue - State: closed - Opened by fabienneM about 7 years ago - 6 comments
Labels: question (please use image.sc!)

#82 - simple tissue detection cannot be trimmed by "Alt+Brush" - bug

Issue - State: closed - Opened by DavidMHaumann about 7 years ago - 1 comment

#81 - Is it possible to import python-opencv contours?

Issue - State: closed - Opened by ElEd2 over 7 years ago - 9 comments
Labels: question (please use image.sc!)

#80 - "Cell detection" variability between tiles

Issue - State: closed - Opened by elijahedmondson over 7 years ago - 5 comments
Labels: question (please use image.sc!)

#79 - Exporting annotations from multiple slides into a single excel spreadsheet

Issue - State: closed - Opened by elijahedmondson over 7 years ago - 3 comments
Labels: question (please use image.sc!)

#78 - Subtracting Brush Annotation

Issue - State: closed - Opened by c-schloss over 7 years ago - 2 comments
Labels: bug

#77 - Is it possible to define a grid and tma spot locations manually?

Issue - State: closed - Opened by rawatenator over 7 years ago - 6 comments
Labels: enhancement, question (please use image.sc!)

#76 - 3rd Party Library Dependencies in Scripts

Issue - State: closed - Opened by c-schloss over 7 years ago - 3 comments
Labels: question (please use image.sc!)

#75 - Undo function

Issue - State: closed - Opened by Junonia over 7 years ago - 7 comments
Labels: enhancement

#74 - Mulithreading bug when reading small images using ImageJ

Issue - State: closed - Opened by petebankhead over 7 years ago - 2 comments
Labels: bug, v0.1.2

#73 - Support for alternative stains in brightfield images

Issue - State: closed - Opened by petebankhead over 7 years ago - 1 comment
Labels: enhancement

#72 - Can not open .jp2 image

Issue - State: closed - Opened by franfcunha over 7 years ago - 2 comments
Labels: file formats

#71 - Saved Annotations

Issue - State: closed - Opened by HMReid over 7 years ago - 7 comments
Labels: bug

#70 - Contour Export

Issue - State: closed - Opened by c-schloss over 7 years ago - 1 comment
Labels: question (please use image.sc!)

#69 - Cell Detection Error On Large TIF File

Issue - State: closed - Opened by c-schloss over 7 years ago - 1 comment
Labels: question (please use image.sc!)

#68 - Imagej Macro Runner on a specific channel

Issue - State: closed - Opened by bpavie over 7 years ago - 7 comments
Labels: enhancement

#67 - Positive pixel count on multiple annotations

Issue - State: closed - Opened by mnolan1989 over 7 years ago - 14 comments
Labels: bug

#66 - Making a dmg file from Linux.

Issue - State: closed - Opened by PeterCha90 over 7 years ago

#65 - Null pointer opening TiFF files

Issue - State: closed - Opened by vaibhavkhanduja over 7 years ago - 3 comments
Labels: file formats

#64 - Positive cell detection

Issue - State: closed - Opened by Kakathrin over 7 years ago - 11 comments

#63 - "No features selected!" when attempting to create detection classifier

Issue - State: closed - Opened by elijahedmondson over 7 years ago - 10 comments
Labels: question (please use image.sc!)

#62 - scripting: export tiles within annotation?

Issue - State: closed - Opened by schmolze over 7 years ago - 6 comments

#61 - Importing/Pregeneration Annotations..

Issue - State: closed - Opened by dgutman over 7 years ago - 4 comments
Labels: question (please use image.sc!)

#60 - Cell detection and tissue detection not compatible at same level of hierarchy

Issue - State: closed - Opened by hartlandj over 7 years ago - 1 comment

#59 - Exporting single cell analysis txt from many cores in TMA

Issue - State: closed - Opened by hartlandj over 7 years ago - 12 comments
Labels: enhancement

#58 - Loading saved project/data

Issue - State: closed - Opened by hartlandj over 7 years ago - 1 comment
Labels: question (please use image.sc!)

#57 - How to continue training saved classifier

Issue - State: closed - Opened by LieseCharlotte over 7 years ago - 8 comments
Labels: question (please use image.sc!)

#56 - Classify

Issue - State: closed - Opened by bpavie over 7 years ago - 10 comments
Labels: enhancement, question (please use image.sc!)

#55 - Java heap space error

Issue - State: closed - Opened by AliSyedRaza over 7 years ago - 2 comments

#54 - OpenWebpageCommand hangs (Linux)

Issue - State: closed - Opened by alanocallaghan over 7 years ago - 1 comment
Labels: bug

#53 - Simple tissue detection for TMA does not work

Issue - State: closed - Opened by LieseCharlotte over 7 years ago - 11 comments

#52 - Different cell detection result categories.

Issue - State: closed - Opened by FridoB over 7 years ago - 3 comments

#51 - libstdc++.so.6 on Ubuntu 14.04 LTS

Issue - State: closed - Opened by rananthan3 over 7 years ago - 2 comments

#50 - Brush tool cannot make annotations in tiled rectangular area.

Issue - State: closed - Opened by c-schloss over 7 years ago - 3 comments
Labels: bug, enhancement, question (please use image.sc!)

#49 - display >3 channels in fluorescence MRXS files

Issue - State: closed - Opened by mariokreutzfeldt over 7 years ago - 5 comments

#48 - TMA detection in CZI format fails also in WSI format with only 1 scene

Issue - State: closed - Opened by DavidMHaumann over 7 years ago - 3 comments
Labels: question (please use image.sc!)

#47 - Add several czi-file Images with 2 scenes each within a Project causes crash

Issue - State: closed - Opened by DavidMHaumann over 7 years ago - 5 comments

#46 - Optimiziation of Positive Cell detection - example Ki67, in H DAB

Issue - State: closed - Opened by DavidMHaumann over 7 years ago - 5 comments
Labels: question (please use image.sc!)

#45 - TMA in CZI format - with 120 scenes brings QuPath down to crash

Issue - State: closed - Opened by DavidMHaumann over 7 years ago - 6 comments

#44 - Tiling with Overlay

Issue - State: closed - Opened by c-schloss over 7 years ago - 3 comments
Labels: question (please use image.sc!)

#43 - CZI support with bioformat

Issue - State: closed - Opened by bpavie over 7 years ago - 1 comment

#42 - Order of listed annotations is unpredictable

Issue - State: closed - Opened by petebankhead over 7 years ago - 4 comments
Labels: enhancement

#41 - QuPath sometimes hangs when making selections amid large numbers of objects

Issue - State: closed - Opened by petebankhead over 7 years ago - 1 comment
Labels: bug

#40 - Labels are not displayed correctly for some image formats

Issue - State: closed - Opened by petebankhead over 7 years ago - 4 comments
Labels: enhancement

#39 - Unexpected behavior when working with classifications with > 2 levels

Issue - State: closed - Opened by petebankhead over 7 years ago - 1 comment
Labels: bug, v0.1.2

#38 - Viewers not removed from internal list after closing

Issue - State: closed - Opened by petebankhead over 7 years ago
Labels: bug

#37 - v0.1.2

Pull Request - State: closed - Opened by petebankhead over 7 years ago

#36 - slide label image

Issue - State: closed - Opened by Phosphuga almost 8 years ago - 4 comments

#35 - Qupath error when changing view on a czi slide

Issue - State: closed - Opened by bpavie almost 8 years ago - 5 comments

#34 - Not opening JPEG-XR compressed CZI

Issue - State: closed - Opened by bpavie almost 8 years ago - 3 comments

#33 - Updated OpenSlide for macOS

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#32 - MRXS slides only opening in lowest resolution (worked in 0.0.7)

Issue - State: closed - Opened by mariokreutzfeldt almost 8 years ago - 10 comments

#31 - v0.1.1

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#30 - v0.1.0 - first release

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#29 - Formatting decimal numbers with dots & commands based on region

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment
Labels: help wanted, question (please use image.sc!)

#28 - v0.0.7

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#27 - Setting symlinks for JEP (Fedora 24)

Issue - State: closed - Opened by penningavery almost 8 years ago - 18 comments

#26 - Brightness & Contrast window , suggestions

Issue - State: closed - Opened by romainGuiet almost 8 years ago - 16 comments
Labels: enhancement

#25 - Measure > Show Annotations not in command history

Issue - State: closed - Opened by lacan almost 8 years ago - 7 comments
Labels: enhancement

#24 - Multiple images in a project with the same name treated as the same

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment

#23 - Image reading issues on macOS - updated OpenSlide binaries required

Issue - State: closed - Opened by petebankhead almost 8 years ago - 2 comments
Labels: bug

#22 - Performance issues related to logging

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment
Labels: bug

#21 - Update to v0.0.6

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#20 - Fixed intensity command bugs for non-brightfield images

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#19 - Updating to v0.0.5

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#18 - Language matters... problems with different location settings

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment
Labels: bug

#17 - Pete superpixels

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#16 - Require ability to sub-classify any detections according to intensity

Issue - State: closed - Opened by petebankhead almost 8 years ago - 12 comments
Labels: enhancement

#15 - Calculate intensity features command does not support tiling, can be confusing

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment
Labels: enhancement

#14 - Cell detection only partially supports fluorescence images

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment
Labels: enhancement

#13 - ImageJ macro runner fails when extracting a large region

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment

#12 - Bio-Formats Extension (0.0.4) does not show up in Extensions menu, cannot be accessed

Issue - State: closed - Opened by arnmayer almost 8 years ago - 8 comments

#11 - Revert "Add a Gitter chat badge to README.md"

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#10 - Add a Gitter chat badge to README.md

Pull Request - State: closed - Opened by gitter-badger almost 8 years ago

#9 - Cannot open .qpdata files if path to the original image has changed

Issue - State: closed - Opened by petebankhead almost 8 years ago - 2 comments

#8 - Pete working

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#7 - Delaunay overlay poor performance, cannot be hidden

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment
Labels: enhancement

#6 - Menubars and shortcuts are confused when ImageJ is open but QuPath is in focus in macOS

Issue - State: closed - Opened by petebankhead almost 8 years ago - 1 comment
Labels: bug

#5 - Extension > Send region to ImageJ sends RGB image with burned in overlays & objects

Issue - State: closed - Opened by sstoma almost 8 years ago - 2 comments

#4 - Update to v0.0.3

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#3 - Updates to 0.0.2

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

#2 - Create Linux binary

Issue - State: closed - Opened by petebankhead almost 8 years ago - 3 comments
Labels: help wanted, question (please use image.sc!)

#1 - Pete working

Pull Request - State: closed - Opened by petebankhead almost 8 years ago

GitHub / qupath/qupath issues and pull requests