Error while running IMCtools about imctools HOT 4 CLOSED

Hi @raman91,

Could you please indicate which version of imctools and python you are using. Please also let me know if this is your own data or the example data/public data for me to reproduce the error. And if there is a longer traceback, please also post it here.
Cheers,

Nils

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Hi @nilseling,

I had this 'Error reading MCD acquisition' problem, too. I am running imctools == 2.x version and python == 3.9.7. This is my code:

from imctools.io.mcd.mcdparser import McdParser
parser = McdParser("LTB_LY_20200522_PDAC_1T_01.mcd")
xml = parser.get_mcd_xml()
session = parser.session
ids = parser.session.acquisition_ids
ac_data = parser.get_acquisition_data(1)

Then I got the error message:

/cluster/apps/anaconda3/2020.02/envs/R-4.1.1/lib/python3.9/site-packages/numpy/core/fromnumeric.py:86: RuntimeWarning: overflow encountered in reduce
  return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
Error reading MCD acquisition: 1

In this case, I have ids = (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38) I tried every id in ac_data = parser.get_acquisition_data() but for all of them I got 'reading MCD acquision' error.

Also, I tried many other .mcd files and there are some errors when reading MCD acquisition. For example, I tried "LTB_LY_20200616_PDAC_2T_01.mcd":

parser = McdParser("LTB_LY_20200616_PDAC_2T_01.mcd")
xml = parser.get_mcd_xml()
session = parser.session
ids = parser.session.acquisition_ids
ac_data = parser.get_acquisition_data(21)

The error is:

Acquisition LTB_LY_20200616_PDAC_2T_01_s0_a21 is emtpy
Error reading MCD acquisition: 21

Also, acquisition 22, 24, 25, 26, 27, 28 is empty while 23 and 29 worked. I am curious why some ROIs cannot be converted to tiff files. Could you please help?

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Hi @WJH58
sorry for the late reply, I completely missed this.
Could you also please test readimc for reading in .mcd and .txt files. We sometimes have the issue that .mcd files are corrupt and you will need to read in the acquisition from the .txt files.

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Closing due to inactivity

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