big-fish

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Is there a way outside of visual inspection to set threshold value for watershed segementation?

1

Is this possible?

buttf7

The function `multistack.from_binary_to_coord()` returns external boundary coordinates. It helps to build back the original mask with `multistack.from_coord_to_surface()`, but might lead to incoherence when the coordinate is directly processing. The user...

Henley13

Plot elbow, return threshold`

1

Hi, Could you edit the plot elbow function so that it returns the detected optimal threshold in addition to the graph?

SachinDavis

Set spot detection threshold based on signal:background

1

Is this already possible? Would be very helpful! j

jstitlow

Increase speed of spot detection

1

Compute time on our HPC ranges from 1-30 minutes, depending on the number of spots. **Any general advice on how to speed this up?** I've split up the analysis using...

jstitlow

when I do a test run with “pytest big-fish” command as they suggest in README docs, I get the error “Permission Error[WinError 32]” . The error stems from the temp...

bhankoma

The function `compute_snr_spots` fails because the type int is not supported anymore in numpy after version 1.24. It should be changed either to np.int64 or np.int32 https://github.com/fish-quant/big-fish/blob/e951ea850b18be4be70c5d0a419ba524c3a59ada/bigfish/detection/utils.py#L582-L583

giocard

hello, We have been successfully using bigfish for a year now with no problems until last week. We are getting this error: IndexError: boolean index did not match indexed array...

LR-MVU