Q: I get the following error when DigitalMicrograph, also known as Gatan Microscopy Suite, software starts up, what should I do?

Most likely, when you upgraded DigitalMicrograph ® software from 3.4.0 to 3.4.1 or higher, you did not uninstall and reinstall Miniconda.DigitalMicrograph 3.4.0 uses an MKL-based NumPy installation.DigitalMicrograph 3.4.1 (and higher) requires an OpenBLAS-based NumPy library instead. To solve this problem, reinstall the DigitalMicrograph virtual environment using DigitalMicrograph 3.4.1.2984 or higher. Any version of DigitalMicrograph before 3.4.1. 2984 requires you to uninstall Miniconda before reinstalling DigitalMicrograph with Python support.

Q: How do I check what Python/NumPy version is used in DigitalMicrograph?

On startup, you can go to the Result window / Debug .

Q: Which Python package manager should I use to install libraries on DigitalMicrograph Python Virtual environment?

In general, we recommend using pip install instead of conda install . DigitalMicrograph uses OpenBLAS-based (NumPy) libraries, and conda install tends to install MKL-based libraries.

Q: Where is Miniconda installation, and where is DigitalMicrograph Python virtual environment installation?

The global (Miniconda) python is installed under C:\ProgramData\Miniconda3\ . DigitalMicrograph Python virtual environment is installed under C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON .

Question 1

I get the following error when DigitalMicrograph, also known as Gatan Microscopy Suite, software starts up, what should I do?

Accepted Answer

Most likely, when you upgraded DigitalMicrograph^® software from 3.4.0 to 3.4.1 or higher, you did not uninstall and reinstall Miniconda.DigitalMicrograph 3.4.0 uses an MKL-based NumPy installation.DigitalMicrograph 3.4.1 (and higher) requires an OpenBLAS-based NumPy library instead.

To solve this problem, reinstall the DigitalMicrograph virtual environment using DigitalMicrograph 3.4.1.2984 or higher. Any version of DigitalMicrograph before 3.4.1. 2984 requires you to uninstall Miniconda before reinstalling DigitalMicrograph with Python support.

Question 2

How do I check what Python/NumPy version is used in DigitalMicrograph?

Accepted Answer

On startup, you can go to the Result window / Debug.

Question 3

Which Python package manager should I use to install libraries on DigitalMicrograph Python Virtual environment?

Accepted Answer

In general, we recommend using pip install instead of conda install. DigitalMicrograph uses OpenBLAS-based (NumPy) libraries, and conda install tends to install MKL-based libraries.

Question 4

I got an error that says, "Cannot run another python script while one running" when running a subsequent python script after using Scipy library in the first Python script, what should I do to solve this?

Accepted Answer

Some Python libraries (such as Scipy, require the script to be run in the main thread. Running a script (that requires it to be run in the main thread) in the background thread will cause the script to hang in the DigitalMicrograph-embedded Python. To solve this, first, try to use Ctrl + Shift + Q to try to kill the script that is running in the background. If this is not successful, you may need to restart DigitalMicrograph. To run these scripts intentionally, please uncheck the checkbox Execute on Background Thread option in the bottom right Python script window the next time you run the script.

Question 5

Where is Miniconda installation, and where is DigitalMicrograph Python virtual environment installation?

Accepted Answer

The global (Miniconda) python is installed under C:\ProgramData\Miniconda3\. DigitalMicrograph Python virtual environment is installed under
C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON.

Question 6

Can we run Python scripts in an external Python environment and call DigitalMicrograph for the internal functions?

Accepted Answer

DigitalMicrograph-Python API is dependent on the DigitalMicrograph application; therefore, it is not possible to execute DigitalMicrograph functions from python outside of the DigitalMicrograph application.

Question 7

Why does DigitalMicrograph use Miniconda and not Anaconda?

Accepted Answer

We chose Miniconda as a starter since it is a small package, does not take long to install, and it gives users the option to expand it when needed by using the pip install commands.

Question 8

Can I use some other Python software (not Miniconda)?

Accepted Answer

Yes, however, you do need to be careful about the versions that you are using. You should make sure you are using Python version 3.10 and NumPy version 1.23.5. Minor changes to Python (e.g., 3.10.x) and NumPy (e.g., 1.23.x) should also work but can’t be guaranteed. The default python used is Miniconda’s DigitalMicrograph Python Virtual environment (GMS_VENV_PYTHON). You can change to use some other Python software in the Global Info dialog (File / Global Info) and restart DigitalMicrograph.

Question 9

Where can I find a list of all the available python commands for DigitalMicrograph?

Accepted Answer

Complete lists of all DigitalMicrograph-specific python commands that can be used in the embedded python interpreter in DigitalMicrograph can be found in the built-in DigitalMicrograph help. This can be accessed from the Help / Search… menu command in DigitalMicrograph or as a PDF in the Gatan documentation folder on a PC where DigitalMicrograph has been installed ( C:\ProgramData\Gatan\Documentation\PythonReference.pdf ).

Question 10

How do I find out if OpenBLAS or MKL-based NumPy is installed in the DigitalMicrograph virtual environment?

Accepted Answer

(The example shown here is an OpenBLAS based NumPy installation.)

Launch Anaconda in administrator mode
Activate GMS_VENV_PYTHON virtual environment :
(base) C:\WINDOWS\system32>activate GMS_VENV_PYTHON

Start python interpreter:
(GMS_VENV_PYTHON) C:\WINDOWS\system32>python
Python 3.7.2 (default, Feb 21 2019, 17:35:59) [MSC v.1915 64 bit (AMD64)] :: Anaconda, Inc. on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> numpy.showConfig()
blas_mkl_info:
NOT AVAILABLE
blis_info:
NOT AVAILABLE
openblas_info:
library_dirs = ['C:\projects\numpy-wheels\numpy\build\openblas_info']
libraries = ['openblas_info']
language = f77
define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
library_dirs = ['C:\projects\numpy-wheels\numpy\build\openblas_info']
libraries = ['openblas_info']
language = f77
define_macros = [('HAVE_CBLAS', None)]
lapack_mkl_info:
NOT AVAILABLE
openblas_lapack_info:
library_dirs = ['C:\projects\numpy-wheels\numpy\build\openblas_lapack_info']
libraries = ['openblas_lapack_info']
language = f77
define_macros = [('HAVE_CBLAS', None)]
lapack_opt_info:
library_dirs = ['C:\projects\numpy-wheels\numpy\build\openblas_lapack_info']
libraries = ['openblas_lapack_info']
language = f77
define_macros = [('HAVE_CBLAS', None)]

Question 11

If I am using MKL-based libraries, how do I change to use OpenBLAS-based libraries for all packages (from Anaconda GMS_VENV_PYTHON prompt):

Accepted Answer

(GMS_VENV_PYTHON) C:\WINDOWS\system32>conda install conda-forge::blas=*=openblas

After invoking the above command, invoke “pip install XXX” where XXX is a python library.

Question 12

How do I use the MKL-based library for NumPy?

Accepted Answer

You really shouldn’t, MKL-based libraries are not supported at this time. However, if you insist, you can use the following command.

(GMS_VENV_PYTHON) C:\WINDOWS\system32>conda install numpy

The conda package manager will update all other affected packages to use MKL-based packages.

Note the MKL-based NumPy is not supported, and we have observed problems when invoking FFT related functions.

Question 13

How do I verify the conda environment is installed correctly via conda info or conda list?

Accepted Answer

The conda list will list out all packages info that are installed in the conda environment. There should not be errors in either of these commands.

(GMS_VENV_PYTHON) C:\WINDOWS\system32>conda info

active environment : GMS_VENV_PYTHON
active env location : C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON
shell level : 2
user config file : C:\Users\wlei\.condarc
populated config files :
conda version : 4.8.3
conda-build version : not installed
python version : 3.7.1.final.0
virtual packages : __cuda=9.2
base environment : C:\ProgramData\Miniconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\ProgramData\Miniconda3\pkgs
C:\Users\wlei\.conda\pkgs
C:\Users\wlei\AppData\Local\conda\conda\pkgs
envs directories : C:\ProgramData\Miniconda3\envs
C:\Users\wlei\.conda\envs
C:\Users\wlei\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.8.3 requests/2.21.0 CPython/3.7.1 Windows/10 Windows/10.0.18362
administrator : True
netrc file : None
offline mode : False
(GMS_VENV_PYTHON) C:\WINDOWS\system32>conda list

# packages in environment at C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON:
#

# Name	Version	Build Channel
_tflow_select	2.2.0	eigen
absl-py	0.9.0	py37_0
asn1crypto	1.3.0	py37_0
astor	0.8.1	pypi_0 pypi
blas	1.0	mkl

Question 14

I am using DigitalMicrograph 3.4.1. I am having some trouble installing Tensorflow 2.10. Is it supported by DigitalMicrograph 3.4.1?

Accepted Answer

Yes, it is supported. You will need to install all the pre-requisites before pip install tensorflow command:

The pre-requisites are: https://www.tensorflow.org/install/gpu

CUDA Toolkit 10.2 version: https://developer.nvidia.com/cuda-downloads?target_os=Windows&target_arch=x86_64&target_version=10&target_type=exenetwork

Visual Studio 2015-2019 x86 and x64 redistributable: https://learn.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist?view=msvc-170#latest-microsoft-visual-c-redistributable-version

Use pip install tensorflow to install the latest tensorflow (currently 2.10).

Sometimes, the user may see an error with the wrong h5py version, use pip uninstall h5py, and pip install h5py to install the required version.

Question 15

When I try to use Ctrl + Shift + Q to kill a running script, I got the following error. What should I do?

Accepted Answer

Some operation in your script is holding onto the Python Global Interpreter Lock and not releasing it, preventing Ctrl + Shift + Q from terminating the script. If Ctrl + Shift + Q does not work, then you may need to restart DigitalMicrograph.

Python scripting FAQs