SchmollerLab/Cell_ACDC issues and pull requests

#586 - Call `core.preprocess_video_from_recipe` in Custom pre-process utility

Issue - State: open - Opened by ElpadoCan about 1 month ago

#585 - Long text messagebox recognise if scrollbar is required

Issue - State: open - Opened by ElpadoCan about 1 month ago

#584 - Custom pre-process utility enhancements

Issue - State: open - Opened by ElpadoCan about 1 month ago
Labels: :balloon: Enhancement

#583 - Utility to run batch pre-processing based on recipe

Issue - State: open - Opened by ElpadoCan about 2 months ago
Labels: :moon: New utility

#582 - Fucci utility must check basicpy installation if requested

Issue - State: open - Opened by ElpadoCan about 2 months ago
Labels: :balloon: Enhancement

#581 - Remove `Filters` menu and add `Pre-processing` sub-menu in the `Image` menu

Issue - State: open - Opened by ElpadoCan about 2 months ago
Labels: :balloon: Enhancement

#580 - Release Cell-ACDC on conda-forge

Issue - State: open - Opened by ElpadoCan about 2 months ago
Labels: :hammer: Build

#579 - Undo (Ctrl+Z) after annotating division in cca mode does not correctly restores will_divide column

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

#578 - Add object count dialogue

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

#577 - Pre-compute object contours and pairings when switching to cca mode

Issue - State: closed - Opened by ElpadoCan 2 months ago - 1 comment
Labels: :balloon: Enhancement

#576 - Problem processing .czi files

Issue - State: open - Opened by jordanyx 3 months ago - 1 comment
Labels: :bug: Bug

#575 - Separating objects on already visited frame should not trigger tracking on all object only new ones

Issue - State: closed - Opened by ElpadoCan 3 months ago
Labels: :bug: Bug

#574 - Warn that the chosen ID in manually editing ID is already in use

Issue - State: closed - Opened by ElpadoCan 3 months ago
Labels: :balloon: Enhancement

#573 - Manually editing ID should suggest a new unique ID

Issue - State: closed - Opened by ElpadoCan 3 months ago
Labels: :balloon: Enhancement

#572 - Search object ID also through time

Issue - State: closed - Opened by ElpadoCan 3 months ago
Labels: :balloon: Enhancement

#571 - fix: small inconstancy errors in Normal division: lineage tree

Pull Request - State: closed - Opened by Teranis 3 months ago

#570 - fix: added r in front of regex strings

Pull Request - State: closed - Opened by Teranis 3 months ago

#569 - Seg for lost IDs and tooltips

Pull Request - State: closed - Opened by Teranis 3 months ago

#568 - Show prepped positions when switching positions with Shift+P in data prep

Issue - State: closed - Opened by ElpadoCan 3 months ago - 1 comment
Labels: :balloon: Enhancement

#567 - Automatically test alternative javabridge pre-compiled files

Issue - State: open - Opened by ElpadoCan 3 months ago
Labels: :balloon: Enhancement

#566 - Error when tracking sub-cellular objects with utility and "Re-label sub-cellular objects before tracking" active

Issue - State: closed - Opened by ElpadoCan 4 months ago
Labels: :bug: Bug

#565 - Custom LUT levels for overlay channels

Issue - State: closed - Opened by ElpadoCan 4 months ago
Labels: :balloon: Enhancement

#564 - Download and test with timelapse example fails

Issue - State: open - Opened by bentaculum 4 months ago - 1 comment
Labels: :bug: Bug

#563 - New segmentation models

Issue - State: open - Opened by ElpadoCan 4 months ago
Labels: :rocket: New feature

#562 - Custom "Key+Click" for delete object

Issue - State: closed - Opened by ElpadoCan 4 months ago
Labels: :balloon: Enhancement

#561 - Separate cells in 3D segmentation

Issue - State: open - Opened by ElpadoCan 4 months ago
Labels: :rocket: New feature

#560 - Export to video on mac fails

Issue - State: open - Opened by ElpadoCan 4 months ago
Labels: :bug: Bug

#559 - small changes for clarity

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

#558 - Failed exporting to video not reported

Issue - State: open - Opened by ElpadoCan 4 months ago
Labels: :bug: Bug

#557 - Do not disable tools in max projection if segmentation is 2D

Issue - State: closed - Opened by ElpadoCan 4 months ago
Labels: :bug: Bug

#556 - Second viewer window not working

Issue - State: open - Opened by ElpadoCan 4 months ago
Labels: :bug: Bug

#555 - Allow to view isometric z planes

Issue - State: open - Opened by ElpadoCan 4 months ago
Labels: :balloon: Enhancement

#554 - Small fixes for ruler in gui and saving npz in resize

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

#553 - Auto scale LUTs

Issue - State: closed - Opened by ElpadoCan 5 months ago
Labels: :balloon: Enhancement

#552 - ERROR Manual bud seperation tool

Issue - State: closed - Opened by AlissaFinster 5 months ago - 3 comments
Labels: :bug: Bug

#551 - Bug fixes and additional functionality for Normal Division: Lineage Tree, refactor setTitleText

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

#549 - Switching planes with overlay on causes overlay to be active when going back to xy

Issue - State: closed - Opened by ElpadoCan 5 months ago
Labels: :bug: Bug

#548 - Viewing segmentation contours in other planes (xz and yz)

Issue - State: closed - Opened by ArohiKhurana 5 months ago
Labels: :balloon: Enhancement

#547 - Error received while shifting from xz plane to xy plane

Issue - State: closed - Opened by ArohiKhurana 5 months ago
Labels: :bug: Bug

#546 - "Annotate cell as dead" gets removed from marked cell after certain actions

Issue - State: closed - Opened by Teranis 6 months ago - 1 comment
Labels: :bug: Bug

#545 - Title now has tooltip so you can view full ID lists and posData.tracked_lost_centroids[frame_i] fix

Pull Request - State: closed - Opened by Teranis 6 months ago

#544 - When displaying lost IDs, acc. missing IDs etc. in the title, one can now hover over it to see untrimmed lists

Pull Request - State: closed - Opened by Teranis 6 months ago - 1 comment

#543 - Save model used and parameters of model for segmentation and tracking

Issue - State: closed - Opened by Teranis 6 months ago - 1 comment
Labels: :balloon: Enhancement

#542 - Error when trying to edit scale bar properties

Issue - State: closed - Opened by ElpadoCan 6 months ago
Labels: :bug: Bug

#541 - Trackastra as real-time tracker

Issue - State: open - Opened by ElpadoCan 7 months ago - 1 comment
Labels: :rocket: New feature, :sleeping: Inactive

#540 - Loading other position of same file (Shift+P) in dataprep bug

Issue - State: open - Opened by Beno71 7 months ago - 1 comment
Labels: :bug: Bug, :sleeping: Inactive

#539 - Add trackastra tracker

Issue - State: closed - Opened by ElpadoCan 7 months ago
Labels: :rocket: New feature

#538 - Propagating deletion of cells causes errors

Issue - State: closed - Opened by Teranis 7 months ago - 2 comments
Labels: :bug: Bug

#537 - Minor bug fixes and improvements for symmetrical and resize

Pull Request - State: closed - Opened by Teranis 7 months ago

#536 - Fiji macros should save additional metadata

Issue - State: closed - Opened by ElpadoCan 7 months ago
Labels: :balloon: Enhancement

#535 - Skipping alignment in dataprep takes too long

Issue - State: closed - Opened by ElpadoCan 7 months ago
Labels: :balloon: Enhancement

#534 - 0 values were rendered by ACDC when measuring fluorescent signals.

Issue - State: open - Opened by CorneliusWang753 7 months ago - 2 comments
Labels: :sleeping: Inactive

#533 - Utility to resize images (up or downscale)

Issue - State: closed - Opened by ElpadoCan 7 months ago
Labels: :rocket: New feature, :moon: New utility

#532 - Normal division tracker should ask to save annotations or not when re-tracking in GUI

Issue - State: closed - Opened by ElpadoCan 7 months ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#531 - Dataprep save alignment only if user clicks on save button

Issue - State: closed - Opened by ElpadoCan 7 months ago
Labels: :balloon: Enhancement

#530 - Could not install on macOS 10.14.6

Issue - State: closed - Opened by jacobmhkim 7 months ago - 16 comments
Labels: :bug: Bug

#529 - Extended support for normal division tracker

Pull Request - State: closed - Opened by Teranis 7 months ago

#528 - Add skip segmentation button to perform only tracking in segmentation module

Issue - State: closed - Opened by ElpadoCan 7 months ago
Labels: :balloon: Enhancement

#527 - Allow saving and loading SAM embedding s

Issue - State: open - Opened by ElpadoCan 7 months ago - 1 comment
Labels: :sleeping: Inactive

#526 - Utility to convert ImageJ ROI files to segmentation files

Issue - State: closed - Opened by ElpadoCan 7 months ago
Labels: :balloon: Enhancement, :moon: New utility

#525 - Allow specifying Fiji location in case already present on macOS

Issue - State: open - Opened by ElpadoCan 8 months ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#523 - Export to Video does not work when starting from frame that is not current one

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :bug: Bug

#522 - Drag timestamp and scale bar relative to click position

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :balloon: Enhancement

#521 - Timestamp is not removed

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :bug: Bug

#520 - Create data structure on macOS by automatic downloading Fiji.app and run macro headless

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :rocket: New feature

#519 - New tracker tracking first groups and then objects relative to each other within groups

Issue - State: open - Opened by ElpadoCan 9 months ago - 1 comment
Labels: :rocket: New feature, :sleeping: Inactive

#517 - Export to video scrolling through z-slices

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :balloon: Enhancement

#516 - Visualization bug manual background

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :bug: Bug

#515 - Allow saving multiple crops in different folders

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :rocket: New feature

#514 - Export to video

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :rocket: New feature

#513 - Add timestamp

Issue - State: closed - Opened by ElpadoCan 9 months ago
Labels: :rocket: New feature

#512 - Detect time points split into multiple files and recommend best course of action

Issue - State: closed - Opened by ElpadoCan 10 months ago - 1 comment
Labels: :rocket: New feature

#511 - Error in opening folder for segmentation

Issue - State: open - Opened by NidhiChopdekar 10 months ago - 3 comments
Labels: :bug: Bug, :sleeping: Inactive

#510 - How to convert npz to COCO format

Issue - State: closed - Opened by ptlzon 10 months ago - 2 comments
Labels: :rocket: New feature, :sleeping: Inactive

#509 - Error in function `gui_mouseReleaseEventImg1` v1.4.27

Issue - State: closed - Opened by Akankshazmaze 10 months ago - 14 comments
Labels: :bug: Bug

#508 - Launch Cellpose GUI from Cell-ACDC GUI

Issue - State: closed - Opened by ElpadoCan 10 months ago
Labels: :rocket: New feature

#507 - Allow selecting which columns to add from `acdc_output` to concatenated spotMAX files

Issue - State: closed - Opened by ElpadoCan 10 months ago
Labels: :balloon: Enhancement

#506 - Expand label issues

Issue - State: closed - Opened by ElpadoCan 10 months ago
Labels: :bug: Bug, :balloon: Enhancement

#504 - Expand shrink label in timelapse keeps wrong last object

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :bug: Bug

#503 - Allow applying filters permanently gui

Issue - State: open - Opened by ElpadoCan 11 months ago - 1 comment
Labels: :balloon: Enhancement, :sleeping: Inactive

#502 - Add points layer cursor only when add by clicking button is active

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :balloon: Enhancement

#501 - Add points layer new id with left-click does not work

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :bug: Bug

#500 - Add points by clicking new functionalities

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :balloon: Enhancement

#499 - Handle Spacing parameters for trackpy differently?

Issue - State: open - Opened by Beno71 11 months ago - 1 comment
Labels: :balloon: Enhancement

#498 - For 3D segm, draw ID on center of z-slice only if visible

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :balloon: Enhancement

#497 - Improvement on how to handle IDs of first frame when tracking in the GUI

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :balloon: Enhancement

#496 - "Add points layer" function permanently changes mouse cursor

Issue - State: open - Opened by Beno71 11 months ago - 1 comment
Labels: :bug: Bug

#495 - Errors in `workers.trackingWorker` are not raised

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :bug: Bug

#494 - Add trackpy `search_radius` docstring

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :balloon: Enhancement

#493 - Switching plane not functional with 4D data

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :bug: Bug

#492 - Compute metrics utilities when z-slice was not selected in dataprep crashes

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :bug: Bug

#491 - Annotate lost objects in 4D only on visualized z-slice

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :balloon: Enhancement

#490 - Cropping causes collapsed shape in ImageJ

Issue - State: closed - Opened by ElpadoCan 11 months ago - 1 comment
Labels: :balloon: Enhancement

#489 - Improve handling of data-prep ROIs

Issue - State: closed - Opened by ElpadoCan 11 months ago - 3 comments
Labels: :balloon: Enhancement

#488 - Docs terminal Screenshots not found

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: documentation

#487 - Crop number of z-slices issues

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :bug: Bug, :balloon: Enhancement

#486 - Line breaks are not present on add custom measurement messagebox

Issue - State: closed - Opened by ElpadoCan 11 months ago
Labels: :bug: Bug

#485 - [TEST]: test `load.loadData.isRecoveredAcdcDfPresent` and why autosave is saving same cca_df

Issue - State: closed - Opened by ElpadoCan 11 months ago

#484 - Error when using Gaussian filter in GUI

Issue - State: closed - Opened by ElpadoCan 12 months ago
Labels: :bug: Bug

#483 - HTTP Error 500: INTERNAL SERVER ERROR when loading omnipose model

Issue - State: closed - Opened by ptlzon 12 months ago - 11 comments
Labels: :bug: Bug

GitHub / SchmollerLab/Cell_ACDC issues and pull requests