Wish-List

[straussmaximilian]

Current (pot. incomplete) wish-list and known bugs, strike-through is done.

Nice to have

• 2D/3D Implementation for Phasor
• Importer/Exporter for Thunderstorm
• Implement HDBSCAN for Clustering
• Create a model from existing data for simulation optimization
• Open-File resets Window
• Support for non-ome-tif
• Remember last working directory for all modules
• Slider for Localize and better arrow functions (e.g., shift + arrow moves ten frames)
• Precise Filtering in Localize
• Chromatic Aberration Correction
• Drift correction in z
• Documentation (FRET)
• Make undrift by file usable with own output drift files
• one-click Installer with GPU Support
• Support for custom colormaps
• Speed Mode for large datasets (i.e., only render every tenth localization)

Room for improvement

• Update from PyQt4 to PyQt5
• Speed up 3D display
• Work on documentation
• Suppress / Fix warnings for terminal version
• Speed up some of the functions with GPU (e.g. rendering images)

Known bugs:

• Freezing MLE Fits
• Fitting Errors in Mac Os X
• RCC can fail
• Resizing a dataset with groups crashes Picasso window
• Exporting large images when having little RAM can cause problems
• Indexing for picked localizations is sometimes not consistent, i.e., when picking, selecting pick similar, linking and saving pick localizations could cause an error as the non-linked localizations are saved
• Exporting of images can cause errors on low-memory PCs as the memory limit can be reached for large oversampling
• Resizing the main window crashes the application when having a dataset with groups

Feel free to comment and add or open a new issue. I'll try to keep this list up to date.

[cleterrier]

Sorry didn't see this before opening issue on ThunderSTORM export.

A small thing that would be nice is to have the settings of localize/render etc remembered between sessions (even from days to days). At least the camera parameters could be stored in a file because they are not likely to change from one day to another for most people.

Another thing: A way in the GUI to process just a part of a raw sequence (a subset of frames with start/stop boxes) for testing.

[straussmaximilian]

What settings would you recommend to be saved?
As for the camera parameters, we have implemented a camera config. The idea is that one defines default cameras and Picasso automatically uses the respective sensitivity values. I made a wiki entry for clarification. https://github.com/jungmannlab/picasso/wiki/Localize

For the GUI process: Do you have any particular features in mind? At some point, I thought of making a speed mode that only uses x % of all localizations for display / algorithms. Is that something you had in mind?

[cleterrier]

Great for the camera, will look into it. For the partial processing, I was thinking simple start/stop frame boxes. It can be useful to process part of the whole sequence, for testing. Another use case is when you want to exclude some frames at the begining (like 100) because initial blinking is too dense, which occurs sometimes in STORM.

[joschnitzbauer]

@cleterrier this type of filtering is conveniently done with “Picasso Filter”. Open the locs file, select column header “frame”, make a histogram and click-drag the region of the histogram you want to keep.
you still have to Localize in frames you might not be interested in, but that hopefully does not take long.
You can also filter in two dimensions at the same time with a 2d histogram (click on two column headers while pressing ctrl), and make a 2d histogram.
Hope this helps!

[cleterrier]

Thanks for the information, I will try that. Is there a way to filter precisely at defined values? It's usually difficult to do by clicking on an histogram.

Once one knows precisely what type of filtering is wanted, having an expression box allowing to rapidly filter on multiple conditions, with precise values would be great. There is something like this in ThunderSTORM, you can do all your cleanup in one step with something like "photons>1000 & photons<100000 & length<10" (where "photons" and "length" are column headers). Maybe something like that could be added to the render module, similarly to the expression box in the localize module?

[straussmaximilian]

I like the idea of having a a precise filter with exact settings. I'll add this to the wishlist.

[cleterrier]

Cool, thanks!