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Please join this forum to discuss usage and development of SIMA and ROI Buddy. By joining, you will automatically be registered for email notifications announcing releases of new versions of the SIMA package and ROI Buddy GUI.

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Alisa Omelchenko3

11/16/19

Motion Correction Error Help

Hey Jeff! Thank you for your quick reply! I changed the sequences to what you suggested and added a

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Motion Correction Error Help

Hey Jeff! Thank you for your quick reply! I changed the sequences to what you suggested and added a

11/16/19

2/26/18

Re: [sima-users] OSError while applying motion correction

Hi Sahar, Sequence.create should not actually create the sequence.pkl file. That happens when you

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Re: [sima-users] OSError while applying motion correction

Hi Sahar, Sequence.create should not actually create the sequence.pkl file. That happens when you

2/26/18

madineh sarvestani

11/7/16

Issue on importing sima, windows

I'm having issues importing Sima after install. I've got a 64bit Windows 7 machine, running

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Issue on importing sima, windows

I'm having issues importing Sima after install. I've got a 64bit Windows 7 machine, running

11/7/16

Nathan Danielson

9/8/16

SIMA 1.3.2 & ROI Buddy Release

We have just released SIMA 1.3.2. This new version includes: Docker image with SIMA pre-installed EC2

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SIMA 1.3.2 & ROI Buddy Release

We have just released SIMA 1.3.2. This new version includes: Docker image with SIMA pre-installed EC2

9/8/16

ragunatha...@gmail.com, Patrick Kaifosh3

7/25/16

Using SIMA for analyzing calcium activity in astrocytic processes

Hi Patrick, Thanks for your reply. Best Regards, Padmashri On Saturday, July 23, 2016 at 3:46:59 PM

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Using SIMA for analyzing calcium activity in astrocytic processes

Hi Patrick, Thanks for your reply. Best Regards, Padmashri On Saturday, July 23, 2016 at 3:46:59 PM

7/25/16

eltes...@koki.mta.hu, Patrick Kaifosh2

7/2/16

Problem running the example dataset

Just linking this with the discussion on GitHub: https://github.com/losonczylab/sima/issues/215. On

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Problem running the example dataset

Just linking this with the discussion on GitHub: https://github.com/losonczylab/sima/issues/215. On

7/2/16

Matthew Shtrahman, Patrick Kaifosh2

3/20/16

Issues getting SIMA to recognize OpenCV

Hi Matt, I think SIMA may require OpenCV version 2.* ie not version 3.* Hope that helps, Patrick

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Issues getting SIMA to recognize OpenCV

Hi Matt, I think SIMA may require OpenCV version 2.* ie not version 3.* Hope that helps, Patrick

3/20/16

JMPP, Patrick Kaifosh4

3/7/16

Error creating dataset with multipage tiffstack larger than 2GB

Hi Patrick, Thanks very much for the info. Indeed I had seen that issue already and it doesn't

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Error creating dataset with multipage tiffstack larger than 2GB

Hi Patrick, Thanks very much for the info. Indeed I had seen that issue already and it doesn't

3/7/16

Ats, … Kiki Chang6

12/15/15

How can I install ROI buddy in mac ?

Hi, I followed the instructions to download SIMA, all ROI buddy dependencies, and ROIbuddy. But when

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How can I install ROI buddy in mac ?

Hi, I followed the instructions to download SIMA, all ROI buddy dependencies, and ROIbuddy. But when

12/15/15

alexande...@rwth-aachen.de, Patrick Kaifosh2

12/1/15

Error in PlaneCA1PC: no 'createCLAHE'

What version of opencv do you have installed? You may want to check the docs for the different

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Error in PlaneCA1PC: no 'createCLAHE'

What version of opencv do you have installed? You may want to check the docs for the different

12/1/15

Christopher Snyder, Patrick Kaifosh2

11/8/15

Motion correction only succeeds with small ROI

Hi Chris, I think the first hypothesis is more plausible. Currently, our motion correction is not

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Motion correction only succeeds with small ROI

Hi Chris, I think the first hypothesis is more plausible. Currently, our motion correction is not

11/8/15

Marta Gajowa, Patrick Kaifosh2

10/31/15

segmentation method for OGB signal?

Hi Marta, Automatic segmentation is still a rather tricky subject, with some methods working well on

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segmentation method for OGB signal?

Hi Marta, Automatic segmentation is still a rather tricky subject, with some methods working well on

10/31/15

Marta Gajowa, Christopher Snyder2

10/12/15

after motion correction extracting data in tiff format

Hi again Marta, I use .... C=motion_model.correct(...) #motion_model is something like HMM for

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after motion correction extracting data in tiff format

Hi again Marta, I use .... C=motion_model.correct(...) #motion_model is something like HMM for

10/12/15

Christopher Snyder, Patrick Kaifosh2

10/8/15

dask and varying stepsize between channels

Christopher Snyder wrote: > Hi Patrick, > > First of all awesome work. I really like what

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dask and varying stepsize between channels

Christopher Snyder wrote: > Hi Patrick, > > First of all awesome work. I really like what

10/8/15

10/3/15

Multiple processes

I'm encountering problems when calling multiple processes in SIMA. Problems occur with motion

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Multiple processes

I'm encountering problems when calling multiple processes in SIMA. Problems occur with motion

10/3/15

Jack Waters, … Patrick Kaifosh19

10/1/15

failed segmentation with STICA

Problem fixed. I now have ROIs with STICA and the example data set. Read on for an explanation. The

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failed segmentation with STICA

Problem fixed. I now have ROIs with STICA and the example data set. Read on for an explanation. The

10/1/15

Gilles Vanwalleghem, Patrick Kaifosh2

9/22/15

Assertion error while using the PlaneCA1PC

It's hard to tell you much just based on the error message. You could try using pdb and see if

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Assertion error while using the PlaneCA1PC

It's hard to tell you much just based on the error message. You could try using pdb and see if

9/22/15

Chongxi Lai, Patrick Kaifosh2

8/14/15

Visualize the example data and start roi_buddy

If you want to visualize the dataset within Python, you can use the matplotlib package and view such

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Visualize the example data and start roi_buddy

If you want to visualize the dataset within Python, you can use the matplotlib package and view such

8/14/15

Chongxi Lai, Patrick Kaifosh16

8/13/15

Successfully import but can not even load example data, TypeError: 'generator' object is not an iterator

OK. So it looks, like the problem was that PIL was installed and not pillow. Let's then consider

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Successfully import but can not even load example data, TypeError: 'generator' object is not an iterator

OK. So it looks, like the problem was that PIL was installed and not pillow. Let's then consider

8/13/15

7/29/15

SIMA 1.3.0 released

We have just released SIMA 1.3.0. This new version includes: DiscreteFourier2D motion correction

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SIMA 1.3.0 released

We have just released SIMA 1.3.0. This new version includes: DiscreteFourier2D motion correction

7/29/15

Jack Waters, … Matthew Davis10

7/10/15

ROI buddy executable fail

Hey all, Just wanted to report that I experienced the same problems with the .exe files (win7 64,

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ROI buddy executable fail

Hey all, Just wanted to report that I experienced the same problems with the .exe files (win7 64,

7/10/15

Randall Ung, Patrick Kaifosh3

6/29/15

What is calculated for ImagingDataset.extract()?

Thanks Patrick! That makes much more sense. Thanks for the reference too - haven't come across

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What is calculated for ImagingDataset.extract()?

Thanks Patrick! That makes much more sense. Thanks for the reference too - haven't come across

6/29/15

Guida Kancheli, Patrick Kaifosh3

6/20/15

import sima.iterables

Thank you - this solved my problem.

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import sima.iterables

Thank you - this solved my problem.

6/20/15

Rylan Larsen, … erik flister7

6/9/15

DLL issue when importing sima

it looks like this bug i've been chasing down may be related to the solution found in this thread

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DLL issue when importing sima

it looks like this bug i've been chasing down may be related to the solution found in this thread

6/9/15

Jack Waters, Patrick Kaifosh6

6/4/15

Patch for signed integer TIFF files (ScanImage5)

Great! Do you want to submit a pull request to our github project, or would you like us to just copy

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Patch for signed integer TIFF files (ScanImage5)

Great! Do you want to submit a pull request to our github project, or would you like us to just copy

6/4/15

wcy20...@gmail.com, Patrick Kaifosh2

6/2/15

sima.ROI.Nonbooleanmask: unable to convert a non-boolean mask to polygons

Hi, https://drive.google.com/file/d/0B6HcXHKONk3taHJKSVJBdk1wRTg/view?usp=sharing Attached is the

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sima.ROI.Nonbooleanmask: unable to convert a non-boolean mask to polygons

Hi, https://drive.google.com/file/d/0B6HcXHKONk3taHJKSVJBdk1wRTg/view?usp=sharing Attached is the

6/2/15

erik flister, Patrick Kaifosh6

5/24/15

imaging.py has no attribute 'misc'

Hi Erik, We can reopen the issue if the problem occurs generally with IPython. Regarding the other

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imaging.py has no attribute 'misc'

Hi Erik, We can reopen the issue if the problem occurs generally with IPython. Regarding the other

5/24/15

Jeff Zaremba, … Patrick Kaifosh7

5/20/15

Re: How can I visualize signals from the csv file which generated using dataset.export_signals

Most likely this results from an improperly formatted sequences. Can you please check that the

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Re: How can I visualize signals from the csv file which generated using dataset.export_signals

Most likely this results from an improperly formatted sequences. Can you please check that the

5/20/15

Yu Peng, Patrick Kaifosh6

5/9/15

DLL issue for sima 1.2.0

This is confusing, because the line in sima that is triggering the sklearn error is: >>>

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DLL issue for sima 1.2.0

This is confusing, because the line in sima that is triggering the sklearn error is: >>>

5/9/15

5/4/15

builtins error on importing sima

I deleted the Sima directory in 'Site Packages' and installed from scratch (pip install sima)

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builtins error on importing sima

I deleted the Sima directory in 'Site Packages' and installed from scratch (pip install sima)

5/4/15

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