Kernel errors when trying to run CLSMImage

[fluorescence-tools]

Kernel errors when trying to run CLSMImage

[tpeulen]

You should be able to open you file(s) with the Windows tttrlib build in the conda channel (minimum required version 0.0.18)

conda install -c tpeulen/label/nightly tttrlib

as follows

import tttrlib
import pylab as p

ptu_file = "AF555-WGA-1.ptu"
data = tttrlib.TTTR(ptu_file, 'PTU')
reading_parameter = {
    "marker_frame_start": [4],
    "marker_line_start": 1,
    "marker_line_stop": 2,
    "marker_event_type": 15,
    "reading_routine": 'SP8',
	"skip_before_first_frame_marker": True
}

clsm = tttrlib.CLSMImage(data, **reading_parameter)
clsm.fill_pixels(channels=[1], tttr_data=data)
print(clsm.intensity.sum())
p.imshow(clsm.intensity.sum(axis=0))
p.show()

I hope that helps. Thanks a lot for providing a file. This helps to improve the library.

[tpeulen]

It is possible that either

1. the frame marker are not correct (there is no real standard).
2. or there is sth wrong with the version you are using

This cannot be a memory issue as on my 8GB machine I can work with 500MB files.

For development/testing I only had/have a very limited number of test files. You can post a link to file that I can use to fix this issue here. Alternatively you can send me a file/link to my email address ([email protected]). In either case I will fix this issue over the weekend.

[jalexs82]

Thank you. Sent an email with the link.