Ecosyste.ms: Issues

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

GitHub / Jhsmit/ColiCoords issues and pull requests

#126 - Calculating Fluorescence Intensity at poles

Issue - State: open - Opened by itaneja2 about 2 years ago - 1 comment

#125 - Image analysis

Issue - State: closed - Opened by Nico-F3 over 3 years ago - 10 comments

#124 - Azagajewski master - solve trig return correct root

Pull Request - State: open - Opened by Jhsmit over 3 years ago

#123 - solve_trig sometimes returns an incorrect root

Pull Request - State: open - Opened by azagajewski over 3 years ago - 6 comments

#122 - Radial distribution errors over occasional cells

Issue - State: open - Opened by azagajewski over 3 years ago

#121 - Integration of analytical _bot _top by default

Pull Request - State: closed - Opened by Jhsmit over 3 years ago - 2 comments

#120 - Cell _top and _bottom methods fail when cell becomes too vertical

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

#119 - Coordinates _top and _bottom fail when cell becomes too vertical

Issue - State: closed - Opened by azagajewski over 3 years ago - 2 comments

#118 - Not Able to Import mahotas

Issue - State: closed - Opened by nikhilrana015 over 4 years ago - 2 comments

#117 - Implement Cell Width Property

Issue - State: closed - Opened by guyazran over 4 years ago - 1 comment

#116 - Segmentation using Inclusion Body containing E. coli (very bloated cells)

Issue - State: closed - Opened by SandorAlbert almost 5 years ago - 3 comments

#115 - Config

Pull Request - State: closed - Opened by Jhsmit almost 5 years ago - 1 comment

#114 - matplotlib deprecationwarning

Issue - State: open - Opened by Jhsmit about 5 years ago

#113 - symfit deprecationwarning

Issue - State: open - Opened by Jhsmit about 5 years ago

#112 - Installation issue

Issue - State: closed - Opened by gittykhirbat about 5 years ago - 7 comments

#111 - Joining CellLists

Issue - State: open - Opened by Jhsmit about 5 years ago

#110 - Support

Pull Request - State: closed - Opened by Jhsmit about 5 years ago

#109 - added test for postprocessing

Pull Request - State: closed - Opened by Jhsmit about 5 years ago

#108 - Clp tests

Pull Request - State: closed - Opened by Jhsmit about 5 years ago - 1 comment

#107 - Plot tests

Pull Request - State: closed - Opened by Jhsmit about 5 years ago

#106 - implement longitudinal and angular distribution kymographs

Issue - State: open - Opened by Jhsmit about 5 years ago

#105 - storm rendering with guassian normalization

Issue - State: open - Opened by Jhsmit about 5 years ago

#104 - New tests

Pull Request - State: closed - Opened by Jhsmit about 5 years ago

#103 - https://colicoords.readthedocs.io/en/latest/storm_data.html#d-daostorm

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

#102 - 3d daostorm

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

#101 - symfit API changes

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

#100 - Implement radon transform

Issue - State: open - Opened by Jhsmit over 5 years ago
Labels: feature request

#99 - KDE for plotting storm

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

#98 - aligning cells with storm data sets with zero localizations

Issue - State: closed - Opened by Jhsmit over 5 years ago

#97 - IterCellPlot plot storm when first element has no localizations

Issue - State: closed - Opened by Jhsmit over 5 years ago

#96 - 'limit_l' kwarg limits by xc coordinate not lc

Issue - State: closed - Opened by Jhsmit over 5 years ago

#95 - measure_r error messages not helpful

Issue - State: closed - Opened by Jhsmit over 5 years ago

#94 - parrallel hdf5 reading

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

#93 - assertion error validation split

Issue - State: closed - Opened by Jhsmit over 5 years ago

#92 - generalize crop_cell into indexing function

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

#91 - super resolution reconstruction in multicolor

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

#88 - STORM refactor to SMLM

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

#87 - importing from colicoords.plot override plotting defaults

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

#86 - method 'box' vs 'gauss' in CellImageFunction

Issue - State: open - Opened by Jhsmit almost 6 years ago

#85 - test custom minimize functions

Issue - State: open - Opened by Jhsmit almost 6 years ago

#84 - bounds for Powell minimizing

Issue - State: open - Opened by Jhsmit almost 6 years ago

#83 - negative intensity values in generated storm data

Issue - State: closed - Opened by Jhsmit almost 6 years ago

#82 - initialize cell with 64 bit binary image

Issue - State: closed - Opened by Jhsmit almost 6 years ago

#81 - Memory usage of optimize_mp increases over time

Issue - State: open - Opened by Jhsmit almost 6 years ago - 2 comments

#79 - add 'limit_l' kwarg for hist_r_dist plotting option

Issue - State: open - Opened by Jhsmit almost 6 years ago

#78 - wrong x units on histogramming storm data

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

#77 - classical spatial dist for storm data

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

#76 - Typecheck CellPlot / CellListPlot argument

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

#75 - CellList optimize optionally skip over erros and report

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

#74 - Docs for chained minimization is wrong

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

#73 - Plotting needs major reworking

Issue - State: open - Opened by Jhsmit about 6 years ago - 1 comment
Labels: enhancement

#72 - norm_y on radial distribution should norm between zero and 1?

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

#71 - multiple warnings when using gauss for storm distributions

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

#70 - docs autodoc module not building

Issue - State: closed - Opened by Jhsmit about 6 years ago - 1 comment

#69 - implement __str__ for colicoords.Coords

Issue - State: open - Opened by Jhsmit about 6 years ago
Labels: feature request

#68 - add test for optional modules

Issue - State: closed - Opened by Jhsmit about 6 years ago - 1 comment

#67 - hyperparameter optimization of differential evolution

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

#66 - MINPACK minimizer for cell fitting raises an error

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

#65 - colorbar / scalebar options for CellPlot imshow / plot_storm

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

#64 - tqdm progress bar for aligning cells

Issue - State: closed - Opened by Jhsmit about 6 years ago - 1 comment
Labels: feature request

#63 - storm plot method gauss performance

Issue - State: open - Opened by Jhsmit about 6 years ago - 1 comment

#62 - CellListPlot wrong y label when plotting storm data

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

#60 - add storm / membrane synthesized data methods in SynthCellList

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

#59 - save load synthetic cell data

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

#58 - reduce repo size

Issue - State: closed - Opened by Jhsmit about 6 years ago - 1 comment

#57 - Dev

Pull Request - State: closed - Opened by Jhsmit about 6 years ago

#56 - support crop cell when cropping shape equal to current shape

Issue - State: open - Opened by Jhsmit about 6 years ago - 1 comment

#55 - Error after final image loaded

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

#54 - assertion error single image processing

Issue - State: closed - Opened by Jhsmit about 6 years ago - 1 comment

#53 - l _dist sigma

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

#52 - performance of fluorescence optimizer is slow

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

#51 - Add pyqt 4 support

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

#50 - drawing error 2

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

#49 - overlay drawing errror #1

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

#45 - abstract fit fit_parameters error

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

#43 - basin hop with bounds=none raises an error

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

#41 - dice coefficient for optimizer comparison

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

#38 - storm data loading units

Issue - State: closed - Opened by Jhsmit over 6 years ago

#34 - return value of CellPlot methods

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

#30 - write img metadata to cell object when using data_to_cells

Issue - State: open - Opened by Jhsmit over 6 years ago
Labels: feature request

#29 - save/load cell list doesnt seem to keep the order!

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

#28 - make a logfile upon optimization

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

#25 - metadata support for images

Issue - State: open - Opened by Jhsmit over 6 years ago
Labels: feature request

#24 - write type of optimization metadata to file

Issue - State: open - Opened by Jhsmit over 6 years ago
Labels: feature request

#23 - Parameter allow fixed value

Issue - State: closed - Opened by Jhsmit over 6 years ago - 3 comments

#22 - pixel values to photons

Issue - State: closed - Opened by Jhsmit over 6 years ago - 3 comments
Labels: feature request

#21 - r dist normalization for storm data

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

#20 - diff evoltion optimization for cell coordinate optimizer

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

#17 - progress bar for multiprocessing optimization

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

#16 - differences h5py on unix and windows

Issue - State: closed - Opened by Jhsmit over 6 years ago - 3 comments

#15 - no tkinter on peregrine

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

#14 - futurewarning h5py

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

#13 - cell object cellist object and optimizer object all have optimize methods

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

#12 - data metaclasses transmit their type

Issue - State: closed - Opened by Jhsmit over 6 years ago

#10 - rotation for STORM doenst work anymore

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