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Eric Thomson
@EricThomson
Congratulations on some great software and a great paper @kushalkolar !!!
Kushal Kolar
@kushalkolar
@mjin1812 Did manually remove ROIs in the Mesmerize ROI manager or from the cnmf.estimate object?
2 replies
Irene Ayuso
@AyusoAa
Hi Kushal, congratulations for the paper! I was wondering if it is possible that the MC output file get the name of the orinial file instead of a collection of letters and numbers. When trying a bunch of parameters for CNMF-E, It is very slow to have to check the match between the original filename and the mc filename everytime. Coud you give some tips on how to change that in the code?
Kushal Kolar
@kushalkolar
@mjin1812 I'm not sure what was causing the issue then in that one case but it seems like it only occurred once so I'm not too concerned.
@AyusoAa I'm not sure what you're trying to do. If you use the batch manager interface you don't need to know the uuids for each item to iterate over parameter variants.
WhereWolf72
@WhereWolf72
@kushalkolar Congrats on the paper! I'm having some trouble getting the metadata (specifically the frames per second) to be loaded properly to run CaImAn's CNMF-E. I am almost certain the problem is on my end, but I can't seem to troubleshoot it. The files were acquired via Nikon Elements, so they were originally .nd2 files. I manually added "fps = __" into the metadata for each as our Elements only uses frame acquisition rate (seconds per frame), and then converted to TIFFs via Elements. Finally, I have deinterleaved the two-channel images into just the channel for the calcium imaging using FIJI. In the end, none of the metadata loaders will recognize the image file as containing the fps metadata. Any help or advice would be greatly appreciated, thank you!
Kushal Kolar
@kushalkolar
@WhereWolf72 you can create a json file with the same name as the tiff file that has the structure of the "json_minimal" described here http://docs.mesmerizelab.org/en/master/user_guides/viewer/modules/tiff_file.html#module-tifffile-metadata
2 replies
danielmichaelvirga
@danielmichaelvirga
Hi, is there any way to import an .h5 file which contains all of the Ca2+ imaging data rather than use a .tiff?
Kushal Kolar
@kushalkolar
Serapio M. Baca
@smbaca
Um, so I filled up a drive with the tmp or working directory and changed the path mid-session. After closing everything I can't get mesmerize to open. Can someone point me to the file where I can adjust the directory path so that mesemerize will open?
Kushal Kolar
@kushalkolar
what do you get when you try to launch mesmerize?

Find the mesmerize config.json file and change the "_MESMERIZE_WORKDIR" key.

if you're on Linux or Mac the config file is located in the .mesmerize dir in the home dir. ON windows it's in the user profile dir.

Serapio M. Baca
@smbaca
Thanks for the assist Kushal! Turned out the config.json file was blank. I just copied one from another user on the server and adjusted for my paths and am back up and running.
WhereWolf72
@WhereWolf72
I successfully ran CNMFe for one of my samples as a test and want to optimize my parameters. However, now I am running into a pickling error that I'm not sure how to fix whenever I try to run CNMFe. Any advice would be appreciated. Here's then end of the error code (I can post the entire error if needed): multiprocessing.pool.MaybeEncodingError: Error sending result: '<multiprocessing.pool.ExceptionWithTraceback object at 0x7f4f6cdd3da0>'. Reason: 'PicklingError("Can't pickle <class '_flapack.error'>: import of module '_flapack' failed",)'
2 replies
Charles Warwick
@cawarwick
Hi, I just ran a small test batch through Mesmerize with good results so far (really loving the GUI and the video tutorials, excellent work). However my actual data has multiple Z-planes and despite being reasonably comfortable with the GUI, I cannot figure out how to get the TIFF file importer to recognize my TIFFs as 3D. I searched the docs for a template meta data file for 3d (such as the meta min provided for single plane imaging) and I couldn't find what the metadata should look like in order to format the json appropriately to get the importer to sort the planes correctly. At the moment, I'm using a ThorLabs scope which exports OME Tiffs along with an XML. In one of the video tutorials Kushal mentioned he would provide a link explaining how to add more meta data import methods but I didn't see the link or info about in the docs. Any help would be appreciated, thanks!
Kushal Kolar
@kushalkolar
@cawarwick you don't need additional metadata to import 3D files, if the default tzxy axes order isn't working you can enter the axes order that your data are in:
http://docs.mesmerizelab.org/en/master/user_guides/viewer/modules/tiff_file.html
6 replies
Charles Warwick
@cawarwick
ok, so new issue. If I import the files in the default order tzxy, the image is rotated 90 degrees, which would suggest my files are tzyx and (256X512 (Y,X)) and using a custom order, when I ran the 3D CNMF, the ROIs appear to be rotated 90 degrees and don't align with the image. Did I do something out of the ordinary?
image.png
Kushal Kolar
@kushalkolar
@cawarwick have you tried using tzyx and seeing what the 3D CNMF output looks like?
Kushal Kolar
@kushalkolar
@cawarwick not fully understanding:
If you use the default tzxy what does the CNMF output look like?
If you use tzyx what does the CNMF output look like?
Charles Warwick
@cawarwick
My post was not as clear as it could have been. The default order tzxy makes my image rotated 90 degrees, so I then instead used tzyx which did import it correctly as pictured in the screenshot (that is a horizontal orientation like a widescreen monitor), but the ROIs generated are rotated 90 degrees. For reference, I did not have this happen with a single Z-plane image, but it imported correctly with the default order of txy. I'm not sure why the multiplane image is different, they were both created in ImageJ from the same source file.
Charles Warwick
@cawarwick
e.g. My first batches were with a simpler single-plane image and it ran exactly as I expected with the default order of txy (screenshot is from a single plane image that ran fine). When I then included the other Z-planes in the TIF the order had to be tzyx for it to be oriented correctly.
image.png
Kushal Kolar
@kushalkolar
Did you try CNMF with tzxy ?
Charles Warwick
@cawarwick
Was waiting on that exact batch to finish. So this is the result with tzxy, which is where the image file is rotated 90 degrees (vertical orientation) using the default import settings, and the output is....still rotated. Huh.
image.png
Kushal Kolar
@kushalkolar
strange, I probably have to bugfix this. 3D capabilities were originally tested with a 512x512 stack.
Charles Warwick
@cawarwick
I'll do a fresh batch tomorrow with a new project just in case there is something funky with my settings, but I'll let you know what I see. I tested this with standard CNMF rather than the 3D as well and it seems to do the same thing.
Kushal Kolar
@kushalkolar
if you can share the file, or a short version ~500 frames, of it that would help
Charles Warwick
@cawarwick
Will do, I'll get that you a link to the file either tonight or tomorrow morning.
Kushal Kolar
@kushalkolar
what do you mean by "tested this with standard CNMF ... and it seems to do the same thing"
7 replies
Charles Warwick
@cawarwick
This is the output of 3D CNMF
image.png
Kushal Kolar
@kushalkolar
ok I guess the problem is specific to using standard CNMF on 3D data
Kathryn Salvati
@kas5dv
error in trying to load script editor: Windows OS:
Traceback (most recent call last):
File "C:\Users\kates\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\main_window.py", line 141, in <lambda>
self.ui.actionScript_Editor.triggered.connect(lambda: self.run_module(script_editor.ModuleGUI))
File "C:\Users\kates\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\main_window.py", line 299, in run_module
m = module_class(self, self._viewer)
File "C:\Users\kates\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\script_editor.py", line 27, in init
self.open_temp_script()
File "C:\Users\kates\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\script_editor.py", line 72, in open_temp_script
home_dir = os.environ['HOME']
File "C:\Users\kates\anaconda3\envs\mesmerize\lib\os.py", line 669, in getitem
raise KeyError(key) from None
KeyError: 'HOME'
Kushal Kolar
@kushalkolar
@kas5dv which windows version is this?
1 reply
I'm guessing this is a computer managed by the university or something?
In the console in the mesmerize welcome window can you try:
import os
os.environ['HOME'] = 'C:\\Users\\kates\\'
2 replies
Kushal Kolar
@kushalkolar
@kas5dv Windows is inconsistent with how it sets the HOME env variable, if you don't want to do this each time you launch mesmerize you can HOME systemwide https://phoenixnap.com/kb/windows-set-environment-variable
1 reply
Kushal Kolar
@kushalkolar
Hi everywhere there will be an in-person training event at CCN in NYC for Mesmerize & Caiman June 2-3. More information: https://indico.flatironinstitute.org/event/2800/
Serapio M. Baca
@smbaca
So, mesmerize has been working well with a number of datasets but I keep getting a dimension mismatch error when running cnme following the motion correction.
status: 0
output_info: Traceback (most recent call last):
File "/opt/caiman/caimanvenv/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMFE.py", line 173, in run
cnm.fit(Y)
File "/opt/caiman/CaImAn/caiman/source_extraction/cnmf/cnmf.py", line 627, in fit
self.update_temporal(Yr, use_init=False)
File "/opt/caiman/CaImAn/caiman/source_extraction/cnmf/cnmf.py", line 903, in update_temporal
*self.params.get_group('temporal'))
File "/opt/caiman/CaImAn/caiman/source_extraction/cnmf/temporal.py", line 212, in update_temporal_components
YrA = YA - AA.T.dot(Cin).T
File "/opt/caiman/caimanvenv/lib/python3.6/site-packages/scipy/sparse/base.py", line 359, in dot
return self
other
File "/opt/caiman/caimanvenv/lib/python3.6/site-packages/scipy/sparse/base.py", line 516, in mul
raise ValueError('dimension mismatch')
ValueError: dimension mismatch
Y.shape: [1448, 600, 600]
processing_time: 11.938894434769947
Kushal Kolar
@kushalkolar
@smbaca thanks for reporting this, could you please use the issue tracker and provide all the details in the template.
LrNttn
@LrNttn
image.png
Hi, I just started working with mesmerize so it's probably an easy question. I'm trying to "add to project" but it keeps telling me to wait. Any tips?
Kushal Kolar
@kushalkolar
@LrNttn if your image file is large it will take a while, do you see any messages in the terminal?
LrNttn
@LrNttn
image.png
@kushalkolar, thank you for the fast reply! I let it run overnight but no movement. It looks like it has to do with the metadata. I don't have a separate file. is there a way to add the fps manually?
Kushal Kolar
@kushalkolar
@LrNttn yup that message shows you how to set it
LrNttn
@LrNttn
Thanks! It worked! I still have to get used to use the terminal :)
Kushal Kolar
@kushalkolar
We have a few more slots available for the CaImAn, Mesmerize & FIOLA workshop in June. It will be in-person in NYC. Register by this Sunday! https://indico.flatironinstitute.org/event/2800/
Tawan Tayron Carvalho
@tawantayron
Hello everybody! In CaImAn it is possible to track neurons over several sessions (demo_multisession_registration.ipynb). Is this function implemented in Mesmerize? If yes, does it work with CNMF-e? Thank you very much in advance!
Kushal Kolar
@kushalkolar
Nope not implemented, maybe at the hackathon in June.