Jhsmit/ColiCoords

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Single-cell fluorescence microscopy data analysis

Stars: 26
Forks: 8
Open beginner issues: 0
Indexed issues: 45

Dominant language: Python
License: MIT
Last GitHub push: Jul 4, 2021
Latest indexed: Sep 18, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Open All

45 issues indexed so far

add test for linear interpolation of rdistmodel calls Open

Jhsmit/ColiCoords#18 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
write type of optimization metadata to file Open

feature request

Jhsmit/ColiCoords#24 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
metadata support for images Open

feature request

Jhsmit/ColiCoords#25 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
make a logfile upon optimization Open

Jhsmit/ColiCoords#28 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
write img metadata to cell object when using data_to_cells Open

feature request

Jhsmit/ColiCoords#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
save cell properties and custom arrays to file Open

feature request

Jhsmit/ColiCoords#40 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Allow 3d STORM Open

feature request

Jhsmit/ColiCoords#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
A preview of another channel Open

Jhsmit/ColiCoords#47 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
paintbrush brush size change / brush size squared Open

Jhsmit/ColiCoords#48 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Add pyqt 4 support Open

Jhsmit/ColiCoords#51 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
performance of fluorescence optimizer is slow Open

enhancement

Jhsmit/ColiCoords#52 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
support crop cell when cropping shape equal to current shape Open

Jhsmit/ColiCoords#56 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
save load synthetic cell data Open

Jhsmit/ColiCoords#59 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
add storm / membrane synthesized data methods in SynthCellList Open

Jhsmit/ColiCoords#60 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
plot_r_dist in CellListPlot only print once if using storm incompatible method Open

Jhsmit/ColiCoords#61 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
CellListPlot wrong y label when plotting storm data Open

Jhsmit/ColiCoords#62 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
storm plot method gauss performance Open

Jhsmit/ColiCoords#63 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
colorbar / scalebar options for CellPlot imshow / plot_storm Open

enhancement

Jhsmit/ColiCoords#65 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
hyperparameter optimization of differential evolution Open

Jhsmit/ColiCoords#67 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
implement __str__ for colicoords.Coords Open

feature request

Jhsmit/ColiCoords#69 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Plotting needs major reworking Open

enhancement

Jhsmit/ColiCoords#73 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
CellList optimize optionally skip over erros and report Open

Jhsmit/ColiCoords#75 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
classical spatial dist for storm data Open

Jhsmit/ColiCoords#77 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
add 'limit_l' kwarg for hist_r_dist plotting option Open

Jhsmit/ColiCoords#79 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
scipy 1.2.0 differential evolution result is much worse (and takes less time) Open

Jhsmit/ColiCoords#80 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Memory usage of optimize_mp increases over time Open

Jhsmit/ColiCoords#81 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
bounds for Powell minimizing Open

Jhsmit/ColiCoords#84 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
test custom minimize functions Open

Jhsmit/ColiCoords#85 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
method 'box' vs 'gauss' in CellImageFunction Open

Jhsmit/ColiCoords#86 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
importing from colicoords.plot override plotting defaults Open

Jhsmit/ColiCoords#87 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
STORM refactor to SMLM Open

Jhsmit/ColiCoords#88 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
allow show datapoints for plotting of axial distribution graphs Open

Jhsmit/ColiCoords#89 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
STORM axial distribution plotting should give storm reconstruction result Open

Jhsmit/ColiCoords#90 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
super resolution reconstruction in multicolor Open

Jhsmit/ColiCoords#91 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
generalize crop_cell into indexing function Open

Jhsmit/ColiCoords#92 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
parrallel hdf5 reading Open

Jhsmit/ColiCoords#94 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
KDE for plotting storm Open

Jhsmit/ColiCoords#99 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Implement radon transform Open

feature request

Jhsmit/ColiCoords#100 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
storm rendering with guassian normalization Open

Jhsmit/ColiCoords#105 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
implement longitudinal and angular distribution kymographs Open

Jhsmit/ColiCoords#106 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Joining CellLists Open

Jhsmit/ColiCoords#111 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
symfit deprecationwarning Open

Jhsmit/ColiCoords#113 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
matplotlib deprecationwarning Open

Jhsmit/ColiCoords#114 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Radial distribution errors over occasional cells Open

Jhsmit/ColiCoords#122 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Calculating Fluorescence Intensity at poles Open

Jhsmit/ColiCoords#126 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 18, 2026

Jhsmit/ColiCoords

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