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Kushal Kolar
@kushalkolar
Thanks
mbandet
@mbandet
Hi Kushal, I'm currently using Mesmerize to open a tif, and opening manually defined ROIs in order to have data to work with within Mesmerize. I'm wondering whether there is a way to apply Fissa (https://www.nature.com/articles/s41598-018-21640-2) onto the data for use with Mesmerize?
Kushal Kolar
@kushalkolar
I took a quick look at it and it may be possible. If you install it in the same environment as Mesmerize you can use it through the console.

You can access the image data through the viewer work environment in the viewer console.

See the "Splice img seq" example to see how to access, change or update the image data in the viewer work environment. http://mesmerizelab.org/user_guides/viewer/overview.html#splice-img-seq

Here are examples for how to access the ROI data using the ROI mananger via the viewer console http://mesmerizelab.org/user_guides/viewer/modules/roi_manager.html#console
Simon Daste
@sdaste_gitlab
Hi Kushal: I hd the Matplotlib issue and run the command you provided but I cannot open Mesmerize, I get the following (and long error messages)
(mesmerize) sdaste@MacBook-Pro ~ % export PYTHONPATH=/Users/sdaste/MESmerize
(mesmerize) sdaste@MacBook-Pro ~ % python /Users/sdaste/MESmerize/mesmerize
Loading, please wait...
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #2
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #3
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #4
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #5
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:997: UserWarning: Bad val "qt5" on line #5
"backend: qt5
"
in file "/Users/sdaste/.matplotlib/matplotlibrc"
Key backend: Unrecognized backend string "qt5": valid strings are ['GTK', 'GTKAgg', 'GTKCairo', 'MacOSX', 'Qt4Agg', 'Qt5Agg', 'TkAgg', 'WX', 'WXAgg', 'GTK3Cairo', 'GTK3Agg', 'WebAgg', 'nbAgg', 'agg', 'cairo', 'gdk', 'pdf', 'pgf', 'ps', 'svg', 'template']
(val, error_details, msg))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/dask/config.py:168: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
===== 2020.07.01 23:07:39 =====
Traceback (most recent call last):
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/Users/sdaste/MESmerize/mesmerize/main.py", line 17, in <module>
from mesmerize.common.window_manager import WindowManager
File "/Users/sdaste/MESmerize/mesmerize/init.py", line 1, in <module>
from .analysis import
File "/Users/sdaste/MESmerize/mesmerize/analysis/init.py", line 3, in <module>
from .math import cross_correlation, drfft_dtw, tvregdiff
File "/Users/sdaste/MESmerize/mesmerize/analysis/math/drfft_dtw.py", line 7, in <module>
from ...plotting.variants.timeseries import TimeseriesPlot
File "/Users/sdaste/MESmerize/mesmerize/plotting/init.py", line 2, in <module>
from .widgets import

File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/init.py", line 3, in <module>
from .kshape import KShapeWidget
File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/kshape/init.py", line 1, in <module>
from .widget import KShapeWidget
File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/kshape/widget.py", line 13, in <module>
from . import kshape_process
File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/kshape/kshape_process.py", line 13, in <module>
from tslearn.clustering import KShape
File "/Users/sdaste/MESmerize/tslearn/clustering.py", line 16, in <module>
from tslearn.metrics import cdist_gak, cdist_dtw, cdist_soft_dtw, \
File "/Users/sdaste/MESmerize/tslearn/metrics.py", line 26, in <module>
@njit()
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/decorators.py", line 174, in wrapper
**dispatcher_args)
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/dispatcher.py", line 539, in init
self.targetctx = self.targetdescr.target_context
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/targets/registry.py", line 50, in target_context
return self._toplevel_target_context
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/utils.py", line 353, in get
res
Any idea what it could be ? many thanks!!
Kushal Kolar
@kushalkolar
@sdaste_gitlab thanks for telling me about this. Could you please post this on the issue tracker on GitHub? Also hard to read tracebacks in gitter
Instructions installation for v0.2 aren't up yet btw for Mac and Linux, might be a library issue so it'd still be great if you could post this on the issue tracker
Kushal Kolar
@kushalkolar
Hi everyone, video tutorials for Mesmerize are finally available! Links are here: https://github.com/kushalkolar/MESmerize#video-tutorials
Serapio M. Baca
@smbaca
Are there updated instructions for the mac/Anaconda install? I have caiman running fine in another environment but I get this error trying to install mesmerize with pip: (mesmerize)% pip install mesmerize
ERROR: Could not find a version that satisfies the requirement mesmerize (from versions: none)
ERROR: No matching distribution found for mesmerize
Kushal Kolar
@kushalkolar
try updating pip wheel & setuptools
5 replies
pip install --upgrade pip setuptools wheel
Eric Melonakos
@emelon8
Hi all, can Mesmerize import .avi files into the viewer for analysis? I saw this video (https://www.youtube.com/watch?v=a1UO2-OhIHw), so I know it's possible with some custom code, but I was wondering if it was already supported through the GUI.
Kushal Kolar
@kushalkolar
you can open an .avi video file as a numpy array using skvideo and then follow the rest here to load it in the Viewer. http://docs.mesmerizelab.org/en/master/user_guides/viewer/overview.html#open-image
you can use skvideo.io.vread, make sure to set as_grey to True http://www.scikit-video.org/stable/modules/generated/skvideo.io.vread.html#skvideo.io.vread
Kushal Kolar
@kushalkolar

We are holding a Mesmerize workshop on Dec 1st & Dec 2nd. For more informtaion please see:
https://www.janelia.org/sites/default/files/You%20%2B%20Janelia/Conferences/22.pdf

Register for the workshop by Nov 20 here:
https://www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends

kevinpan0127
@kevinpan0127
Hi!
I am trying to use the motion correction feature in mesmerize but I am getting an error saying File "c:\users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\caiman_motion_correction.py", line 23, in <module>
import caiman as cm
ModuleNotFoundError: No module named 'caiman'
Kushal Kolar
@kushalkolar
Hi @kevinpan0127, replied to your issue on github
kevinpan0127
@kevinpan0127
Hi @kushalkolar, I am now trying to run the CNMF module and i am getting getting stuck with the following message:

RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.

    This probably means that you are not using fork to start your
    child processes and you have forgotten to use the proper idiom
    in the main module:

        if __name__ == '__main__':
            freeze_support()
            ...

    The "freeze_support()" line can be omitted if the program
    is not going to be frozen to produce an executable.

===== 2020.12.27 20:12:44 =====

Is there something that I am doing incorrectly? Thank you!
Kushal Kolar
@kushalkolar
@kevinpan0127 This seems like a Windows multiprocessing issue, can you post and issue with the entire traceback
VivoNeuro
@VivoNeuro
Hi,
I am just installing (win10) mesmerize following the steps on Read the Docs. I did all the 10 steps except 6 (pip install bottleneck==1.2.1, here it sent me a message: Microsoft Visual C++ 14.0 or greater is required; but these 5-6 steps are optional). When I tried to launch mesmerize it sent me: ModuleNotFoundError: No module named 'tslearn.cycc'. Could you help me? Thank you
16 replies
Bilalgp
@Bilalgp
I am having trouble displaying the dF/F in the ROI Manager. Do you know how I can troubleshoot?
image.png
Kushal Kolar
@kushalkolar
you must compute them first, it's one of the caiman modules
Bilalgp
@Bilalgp
Thanks! @kushalkolar !
Is there a way to show rejected components in the ROI manager?
Kushal Kolar
@kushalkolar
@Bilalgp there currently isn't but if you make a feature request on the issue tracker I'll look into it for a future version of mesmerize :)
Bilalgp
@Bilalgp
Great thanks.
I also just noticed for a dataset, the ROIs for the caiman HDF5 file aren't correctly matching with that in Mesmerize (traces are correctly numbered but being for the wrong ROI on the map). I am not sure if this problem is because of my Caiman pipeline so I'll investigate but I thought I should let you know.
1 reply
kevinpan0127
@kevinpan0127
@kushalkolar I was wondering how should I update v0.5.0? thank you very much!
sneezeman
@sneezeman
Hello there!
I'm trying to follow the youtube tutorials, but so far I can't reproduce even the first steps: stimulus import/export and batch motion correction
I'm on Ubuntu 18.04.3, used pip to install mezmerise.
So, problems: when I click on export/import buttons in Stimulus Mapping window, nothing happens, and no error is shown in the console. Otherwise, the Stimulus Mapping works.
With batch processing I can add the tasks, but when I click Start, it looks like it starts to work, but no output appears in the additional console. Again, no errors in the main console.
@sneezeman I've also checked that caiman works in this environment, and it does work
Kushal Kolar
@kushalkolar
@sneezeman the import & export buttons on the stimmapping module are not functional, you can import stimmaps from sources such as csv/xls files using the script editor or enter a stimmap manually.
@sneezeman for the batch manager, make sure your system configuration is setup properly. See the steps at the end of the installation for details.
Bilalgp
@Bilalgp
Hi. I am interested in tracking a specific ROI generated from Caiman on more videos besides the boundaries used in generating that ROI. Is there any way to do this in Mesmerize?
Kushal Kolar
@kushalkolar
@Bilalgp Do you mean that you want to use the ROIs from one video's CNMF(E) output to see the ROIs for performing CNMF(E) on other videos?
Kushal Kolar
@kushalkolar
@Bilalgp
You can seed a CNMF(E) batch item by either:
  1. Passing the UUID of a prior batch item in the same batch to the Ain entry in the CNMF(E) module GUI.
  2. Saving a sparse mask (that can be loaded through numpy.load() in the batch dir with the filename: <item_uuid>.ain
Bilalgp
@Bilalgp
Apologies for the late response. Thank you for the prompt reply. Just to clarify, for the Caiman functions, I should a previous generated Ain variable into the Ain entry in a new analysis? Should the previous Ain variable be loaded from the cnmf class?
Kushal Kolar
@kushalkolar

@Bilalgp
For CNMF:
If you have an Ain array from a cnmf object, just save it using numpy.save(), and place it in the batch path with the filename: <uuid>.ain and check the "Seed components from mask" checkbox in the CNMF params GUI.

For CNMFE:
Currently you can only use ROIs from a previous CNMFE item that already exists in the batch manager. Just enter the UUID of the previous item in the Ain line entry.

14 replies
Bilalgp
@Bilalgp
image.png
kir0ul
@kir0ul:matrix.org
[m]
Hi there, quick question: can I export ROIs and calcium traces with Mesmerize? And if yes in which format(s)?
Kushal Kolar
@kushalkolar
@kir0ul:matrix.org Do you want to save it to a mesmerize project or do you just want to save the work environment in the viewer?
9 replies
kir0ul
@kir0ul:matrix.org
[m]
I'll have a look at that, thanks @kushalkolar!
Kushal Kolar
@kushalkolar
We have an importable VM that you can use to get up & running with Mesmerize within minutes if you don't want to setup virtual/conda envs etc. http://docs.mesmerizelab.org/en/master/user_guides/installation.html#all-platforms
1 reply