How import SerialEM data

[ricounet67]

I am trying to test ETSpy for my research purpose and, since I am a poor python user, I am stucked with some basic features. Indeed, I have tilt series acquired with SerialEM, so I have a mrc stack and the mdoc file associated.

I saw that I can read the SerialEM stack with the command
serie=tomo.io.load_serialem('manips/20240710-hc_aa_1000g-after-annealing/tomo1-2024-07-10/hc_aa_1000g.mrc', 'manips/20240710-hc_aa_1000g-after-annealing/tomo1-2024-07-10/hc_aa_1000g.mrc.mdoc')
One this made I obtain a TomoStack with the right dimensions but I have no tilt angles associated. How can I read the tilt angles from the data ?

I tried also the etspy.io.parse_mdoc('manips/20240710-hc_aa_1000g-after-annealing/tomo1-2024-07-10/hc_aa_1000g.mrc.mdoc') command but I obtain a tuple :
({'PixelSpacing': 36.4912,
'Voltage': 300.0,
'ImageFile': 'hc_aa_1000g.mrc',
'DataMode': 1.0,
'Magnification': 28500.0,
'SpotSize': 3.0,
'Defocus': -23.6507,
'ExposureTime': 1.678},
array([ 6.89979e+01, 6.80020e+01, 6.70040e+01, 6.60041e+01,
6.50067e+01, 6.40083e+01, 6.30084e+01, 6.20080e+01,
6.10091e+01, 6.00068e+01, 5.90079e+01, 5.80075e+01,
5.70081e+01, 5.60072e+01, 5.50088e+01, 5.40070e+01,
5.30066e+01, 5.20077e+01, 5.10073e+01, 5.00069e+01,
4.90070e+01, 4.80071e+01, 4.70063e+01, 4.60069e+01,
4.50060e+01, 4.40071e+01, 4.30067e+01, 4.20059e+01,
4.10060e+01, 4.00061e+01, 3.90062e+01, 3.80063e+01,
3.70059e+01, 3.60060e+01, 3.50057e+01, 3.40063e+01,
3.30059e+01, 3.20060e+01, 3.10056e+01, 3.00062e+01,
2.90073e+01, 2.80069e+01, 2.70075e+01, 2.60077e+01,
2.50087e+01, 2.40084e+01, 2.30080e+01, 2.20076e+01,
2.10097e+01, 2.00088e+01, 1.90084e+01, 1.80100e+01,
1.70096e+01, 1.60088e+01, 1.50104e+01, 1.40075e+01,
1.30086e+01, 1.20097e+01, 1.10098e+01, 1.00094e+01,
9.00907e+00, 8.00772e+00, 7.00832e+00, 6.01087e+00,
5.00855e+00, 4.00866e+00, 3.00975e+00, 2.01084e+00,
1.00997e+00, 1.00845e-02, -9.86875e-01, -1.98725e+00,
-2.98958e+00, -3.98898e+00, -4.98984e+00, -5.98973e+00,
-6.98962e+00, -7.98999e+00, -8.99086e+00, -9.98928e+00,
-1.09887e+01, -1.19881e+01, -1.29889e+01, -1.39879e+01,
-1.49882e+01, -1.59881e+01, -1.69880e+01, -1.79864e+01,
-1.89863e+01, -1.99857e+01, -2.09846e+01, -2.19835e+01,
-2.29844e+01, -2.39843e+01, -2.49827e+01, -2.59826e+01,
-2.69830e+01, -2.79814e+01, -2.89813e+01, -2.99807e+01,
-3.09713e+01, -3.19839e+01, -3.29808e+01, -3.39812e+01,
-3.49792e+01, -3.59820e+01, -3.69804e+01, -3.79808e+01,
-3.89807e+01, -3.99801e+01, -4.09804e+01, -4.19808e+01,
-4.29817e+01, -4.39801e+01, -4.49805e+01, -4.59804e+01,
-4.69798e+01, -4.79816e+01, -4.89795e+01, -4.99760e+01,
-5.09759e+01, -5.19777e+01, -5.29815e+01, -5.39765e+01,
-5.49798e+01, -5.59739e+01, -5.69738e+01, -5.79751e+01,
-5.89750e+01, -5.97802e+01]))
The tilt angles are in the array but I don’t know how to exploit this.

It is really basic questions but I am blocked with them. Can you help me ?

[AndrewHerzing]

There is no need to use the load_serialem function directly as this function is used to read a special subset of SerialEM file where multiple images were stored at each tilt. For conventional SerialEM MRC files as it appears you are using, you can simply call the load function and the reader will handle the tilt assignment.

series = etspy.load('manips/20240710-hc_aa_1000g-after-annealing/tomo1-2024-07-10/hc_aa_1000g.mrc')

If your MRC file still fails to load for some reason, please update this issue with additional detail.

As for the parse_mdoc function, you should not need to use this either. However, just to clarify, this function returns two variables. The first is a metadata dictionary and the second is the tilt array. So, the proper usage is:

metadata, tilts = etspy.io.parse_mdoc('manips/20240710-hc_aa_1000g-after-annealing/tomo1-2024-07-10/hc_aa_1000g.mdoc'

Here is the documentation for the function that describes what it returns:

etspy/etspy/io.py

Lines 114 to 139 in f39ac59

	def parse_mdoc(
	mdoc_file: PathLike,
	series: bool = False,
	) -> Tuple[dict, Union[np.ndarray, float]]:
	"""Parse experimental parameters from a SerialEM MDOC file.
	Parameters
	----------
	mdoc_file
	Name of a SerialEM MDOC file
	series
	If ``True``, the MDOC files originated from a multiscan SerialEM acquisition.
	If ``False``, the files originated from a single scan SerialEM acquisition.
	Returns
	-------
	metadata : dict
	A dictionary containing the metadata read from the MDOC file
	tilt : :py:class:`~numpy.ndarray` or float
	If ``series`` is true, tilt will be a single float value, otherwise
	it will be an ndarray containing multiple tilt values.
	Group
	-----
	io
	"""