SchmollerLab/Cell_ACDC issues and pull requests

#382 - Installing javabridge - did not complete

Issue - State: closed - Opened by makotojohira over 1 year ago - 13 comments
Labels: :bug: Bug, :sleeping: Inactive

#381 - Save mean corrected by background

Issue - State: closed - Opened by ElpadoCan over 1 year ago - 2 comments
Labels: :balloon: Enhancement, :sleeping: Inactive

#380 - Add metrics where background correction is by mean and not median

Issue - State: closed - Opened by ElpadoCan over 1 year ago - 2 comments
Labels: :balloon: Enhancement, :sleeping: Inactive

#379 - Allow setting background per-cell based by dragging the cell segm mask

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :rocket: New feature

#378 - Migrate user profile file by file and show progress in second progressbar

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#377 - Tooltip text is white after switching to light mode

Issue - State: closed - Opened by ElpadoCan over 1 year ago - 1 comment
Labels: :balloon: Enhancement

#376 - Error with About Cell-ACDC menu

Issue - State: closed - Opened by nadaspotmax over 1 year ago - 1 comment
Labels: :bug: Bug

#375 - Utility to count sub-cellular objects

Issue - State: closed - Opened by ElpadoCan over 1 year ago - 1 comment
Labels: :rocket: New feature, :moon: New utility

#374 - Single image view random zooming out

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#373 - Delete objects outside selected segmentation mask

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :rocket: New feature

#372 - Error on hover objects to get properties in dock widget

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#371 - Disable right click menu on scrollbars

Issue - State: closed - Opened by ElpadoCan over 1 year ago

#370 - Automatically initialize models' parameters that have the same name of a metadata.csv entry

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :rocket: New feature

#369 - Allow turning off of lost objects annotations

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#368 - Error when trying to reassign a bud

Issue - State: closed - Opened by Teranis over 1 year ago - 2 comments
Labels: :bug: Bug

#367 - [Build] On macOS install hdf5 with `brew install hdf5` at initialization

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#366 - [Build] Remove `tables` dependency and install it at initialization.

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#365 - Transfer Segmentation mask/outline to next frame if ID is lost by Segmentation Algorithm

Issue - State: open - Opened by ppreith over 1 year ago - 6 comments
Labels: :balloon: Enhancement, :sleeping: Inactive

#364 - Option to select which columns to include in the 'Concatenate acdc output tables' utility

Issue - State: closed - Opened by KurtSchmoller over 1 year ago - 4 comments
Labels: :rocket: New feature

#363 - Crash after starting seg. on multiple frames from GUI

Issue - State: closed - Opened by Teranis over 1 year ago
Labels: :bug: Bug

#362 - The `temp` folder with Cell-ACDC settings should be in the user folder

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#361 - Warning if in cell cycle analysis a bug is paired with a dead cell as mother

Issue - State: closed - Opened by Teranis over 1 year ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#360 - Dark mode colors in Errors summary are a bright white

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#359 - Error when starting cell cycle analysis from a frame that is not the first one

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#358 - Reinitialising last visited frame should not delete non-saved manually segmented objects

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#357 - Error raised when trying to crop in Data Prep after aligning

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#356 - Correctly handle 4D data in segm multiple frames gui

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

#355 - Objects deleted by Del ROIs are still considered new or lost

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#354 - Segment multiple frames in GUI causes critical worker error

Issue - State: closed - Opened by Teranis over 1 year ago
Labels: :bug: Bug

#353 - Error during data prep

Issue - State: closed - Opened by Teranis over 1 year ago
Labels: :bug: Bug

#352 - Del ROI on annotated frames does not work

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#351 - Cancelling addition of del ROI on annotated frames should remove the ROI

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#350 - DeepSea tracker min_size keyword error

Issue - State: open - Opened by zsdqui over 1 year ago - 11 comments
Labels: :bug: Bug, :sleeping: Inactive

#349 - Brush auto-fill holes does not work in 3D segmentation

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#348 - Brush should draw in contours mode if contours are active

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#347 - Add a checkbox to toggle automatic hiding of annotations when hovering with brush

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement

#346 - Utility to save the coordinates of the pixels in each cell

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :balloon: Enhancement, :moon: New utility

#345 - Invert black and white doesn't work

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#344 - Write last commit id in the Help-->About Cell-ACDC menu

Issue - State: closed - Opened by Teranis over 1 year ago - 1 comment
Labels: :balloon: Enhancement

#343 - Contours of objects deleted by the deletion ROI are drawn also on deleted cells

Issue - State: closed - Opened by Teranis over 1 year ago
Labels: :bug: Bug

#342 - Allow moving deleteion ROIs also few pixels outside of the ROI

Issue - State: closed - Opened by Teranis over 1 year ago
Labels: :balloon: Enhancement

#341 - Viewer window in GUI is broken

Issue - State: closed - Opened by Teranis over 1 year ago
Labels: :bug: Bug

#340 - Add possibility to manually enter points by clicking

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :rocket: New feature

#339 - Add to btrack the same parameters of the napari plugin

Issue - State: open - Opened by ElpadoCan over 1 year ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#338 - "Cells in "S/G2/M" disappeared" warning about disapeareance of a cell idex which does not exist

Issue - State: closed - Opened by Teranis over 1 year ago - 1 comment
Labels: :bug: Bug

#337 - Added scripts for correcting bidirectional shift

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

#336 - Errors while adding resizable rectangle to ignore IDs in frames when the later frames have already been visited.

Issue - State: closed - Opened by Teranis over 1 year ago - 1 comment
Labels: :bug: Bug

#335 - Non-critical error fill holes

Issue - State: closed - Opened by Teranis over 1 year ago
Labels: :bug: Bug

#334 - Saving only size measurements results in 0s instead of values

Issue - State: closed - Opened by ElpadoCan over 1 year ago - 2 comments
Labels: :bug: Bug

#333 - Is it possible to export image with segmentation mask to Fiji?

Issue - State: closed - Opened by carolynw898 over 1 year ago - 2 comments
Labels: :question: Question

#332 - Custom annotations on 3D segmented organoids error

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#331 - Napari arboretun error

Issue - State: closed - Opened by ElpadoCan over 1 year ago
Labels: :bug: Bug

#330 - Type error when using trackpy from the Tracking menu in GUI

Issue - State: open - Opened by Beno71 over 1 year ago - 3 comments
Labels: :bug: Bug, :sleeping: Inactive

#329 - Non-critical error regarding pytables

Issue - State: open - Opened by Beno71 over 1 year ago - 1 comment
Labels: :bug: Bug, :sleeping: Inactive

#328 - Non-critical error when launching GUI

Issue - State: closed - Opened by Beno71 over 1 year ago - 2 comments
Labels: :bug: Bug

#327 - Error when running trackpy with default params

Issue - State: open - Opened by Beno71 over 1 year ago - 3 comments
Labels: :bug: Bug, :sleeping: Inactive

#326 - Segmentation job is not cancelled upon aborting segmentation

Issue - State: open - Opened by Beno71 over 1 year ago - 4 comments
Labels: :bug: Bug, :sleeping: Inactive

#325 - Allow key for frame forward/backward to be mapped

Issue - State: closed - Opened by Teranis almost 2 years ago - 2 comments
Labels: :balloon: Enhancement, :sleeping: Inactive

#324 - Delete annotation button message upon closing Cell-ACDC

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :bug: Bug

#323 - NetworkX error when greedily shuffling colormap

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :bug: Bug

#322 - Custom omnipose model support

Issue - State: open - Opened by dimethylglymaxim almost 2 years ago - 5 comments
Labels: :balloon: Enhancement, :sleeping: Inactive

#321 - Replace PyQt5 with qtpy

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :balloon: Enhancement

#319 - Select model list includes trackers

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

#318 - Allow saving only a subset of loaded Positions

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :rocket: New feature, :sleeping: Inactive

#317 - Hovering on ID should not go to center z-slice, only when searching an ID

Issue - State: closed - Opened by ArohiKhurana almost 2 years ago
Labels: :balloon: Enhancement

#316 - Allow loading multiple saved custom annotations at once

Issue - State: closed - Opened by ArohiKhurana almost 2 years ago
Labels: :balloon: Enhancement

#315 - Load custom annotaion does not load the color

Issue - State: closed - Opened by ArohiKhurana almost 2 years ago
Labels: :bug: Bug

#314 - Allow Bayesian Tracker to annotate cell cycle stage

Issue - State: open - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :rocket: New feature, :sleeping: Inactive

#313 - Brush on 3D segm in max-projection causes crashing

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 2 comments
Labels: :bug: Bug, :sleeping: Inactive

#312 - Ensure IDs continuity when tracking partial video

Issue - State: open - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#311 - Allow saving measurements beyond the last visited frame

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :balloon: Enhancement

#309 - Using Python in-built `max` on empty IDs raises ValueError

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :bug: Bug

#308 - Add user set regionprops in post-processing

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :rocket: New feature, :sleeping: Inactive

#307 - Used `with` statement when opening files and refactored `segment()`

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

#306 - Faster actions on large data

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#305 - Creating and opening Positions with different numbers of z-slices is not possible

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :bug: Bug

#304 - Show overlay lut items side by side instead of hiding

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :balloon: Enhancement

#303 - Cell cycle annotation should search in all past frames if a cell was existing

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :rocket: New feature

#302 - Automatic/Manual separation tool - new options

Issue - State: open - Opened by Ciro1990 almost 2 years ago - 2 comments
Labels: :rocket: New feature, :sleeping: Inactive

#301 - Store GUI settings in a configuration file (.ini)

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#300 - Integrate DeepSea model

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :rocket: New feature, :sleeping: Inactive

#299 - Allow objects disappearing and reappearing in cell cycle annotations

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :rocket: New feature

#298 - Faster text annotations and contours layer

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 2 comments
Labels: :rocket: New feature, :sleeping: Inactive

#297 - Add a combobox on Launcher with a list of open windows and a show button

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 2 comments
Labels: :balloon: Enhancement, :sleeping: Inactive

#296 - Warn that do no annotate is active after segmenting

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#295 - Only one color is pre-loaded on multiple overlaid channels

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 2 comments
Labels: :bug: Bug, :sleeping: Inactive

#294 - At the end of concatenation ask the file formats of the output file

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :rocket: New feature, :sleeping: Inactive

#293 - Ask to automatically concatenate measurements of multiple Positions

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#292 - Cellpose modul: Cell_prob_threshold value can not be set negative

Issue - State: open - Opened by dfgdgdfgd almost 2 years ago - 3 comments
Labels: :bug: Bug, :sleeping: Inactive

#291 - Automatically go to next frame where a new object appears

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :rocket: New feature, :sleeping: Inactive

#290 - Load last selection button on set measurements should uncheck/check last selected channels

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :balloon: Enhancement

#289 - Keep two versions of auto-saved recovery files

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 3 comments
Labels: :balloon: Enhancement, :bangbang: Priority, :sleeping: Inactive

#288 - Warn user on closeEvent that autosave worker is still running

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 2 comments
Labels: :balloon: Enhancement, :sleeping: Inactive

#287 - Automatically move z-slice to where the ID is present when searching in 3D segm data

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :balloon: Enhancement

#286 - Data Structure Creation for Multiple-Position File Mixes Up Frames

Issue - State: closed - Opened by AP712 almost 2 years ago - 7 comments
Labels: :bug: Bug

#285 - Clearer and better handling of 0 pixels introduced by alignment

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#284 - Allow alternative readers to BioFormats

Issue - State: open - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement

#283 - After converting .npz to .tif with same channel endname the wrong file gets loaded

Issue - State: closed - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :bug: Bug, :sleeping: Inactive

#282 - [Downstream] Allow loading acdc_output files that ends with different names

Issue - State: open - Opened by ElpadoCan almost 2 years ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#281 - Remove focus from scrollable sliders area to avoid scrolling with keyboard arrows

Issue - State: closed - Opened by ElpadoCan almost 2 years ago
Labels: :bug: Bug

GitHub / SchmollerLab/Cell_ACDC issues and pull requests