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informatics-isi-edu / synspy

Synaptic segmentation and visualization with fluorescence microscopy
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Error in loading synapse segments - strange #27

Closed BDemps closed 7 years ago

BDemps commented 7 years ago

Hi, I get an error that I don't recognize when trying to load the synapses from the ImgZfZdu20161228A6 dataset (see below). One thing that I noticed is that the cropbox definition has a boundary in the X dimension that disagrees with some of the choices of synapses (i.e., some synapses were chosen outside of the cropbox dimension). I'm not sure how this is possible with the launcher program handling everything, but the user who did this data collection did use the software for the before and after images. The before image (A3C) loads synapses fine, while the after (A6C) does not load at all.

Could you look into this, when you have a chance? I'd rather not lose these data, if possible!

errorfor20161228a6

karlcz commented 7 years ago

Before we chase our tails here...

  1. What error message are you seeing that you've never seen before?

  2. Is it possible you revised the crop box after the region was assigned?

  3. Also, what values specifically are out of range (and by how much)?

BDemps commented 7 years ago

(1) "ERROR:Invoking <bound method Canvas.on_key_press of <Canvas (PyQt4) at 0x7f6c11b05990>"

(2) No, i really doubt that I changed it that time. There would have been no reason too, unless this happened when the FScope died, which I don't believe it did until January.

(3) The first 75 or so entries when you've sorted the X column.

On Thu, Jul 6, 2017 at 1:37 PM, Karl Czajkowski notifications@github.com wrote:

Before we chase our tails here...

  1. What error message are you seeing that you've never seen before?

  2. Is it possible you revised the crop box after the region was assigned?

  3. Also, what values specifically are out of range (and by how much)?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_informatics-2Disi-2Dedu_synspy_issues_27-23issuecomment-2D313512434&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=Ik1_EUf3EbZ-Dei5Mg3JJK_1QQ4SRU0TAJVM8t6YA_0&s=FN-DyGchR91t25qrxazkkKIHy5bFMJ9UNL6TIzE0GII&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AbQSt5hMnqnlxo6AGs4MRR-2DJyzOpzaK7ks5sLUWbgaJpZM4OQIbC&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=Ik1_EUf3EbZ-Dei5Mg3JJK_1QQ4SRU0TAJVM8t6YA_0&s=hdp9yvjLPThWZYQ3WIDtjZARwlY78IWWB15KMqI0zqI&e= .

-- William Dempsey, Ph.D. Postdoctoral Scholar Molecular and Computational Biology Dana and David Dornsife College of Letters, Arts and Sciences University of Southern California wdempsey@usc.edu Lab #: 213-821-1818

karlcz commented 7 years ago

is the line before that:

AssertionError: ('CSV dump does not match image analysis!', './ImgZfZdu20161228A6.synapses.csv')

or something very similar?

BDemps commented 7 years ago

Oh, yes

On Jul 6, 2017 2:09 PM, "Karl Czajkowski" notifications@github.com wrote:

is the line before that:

AssertionError: ('CSV dump does not match image analysis!', './ImgZfZdu20161228A6.synapses.csv')

or something very similar?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_informatics-2Disi-2Dedu_synspy_issues_27-23issuecomment-2D313520051&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=_yMTaNh6REuSNjXkVnyyasYyxYJXCEVZL5lJGMxMFyI&s=mZHcqRi2Dtr98Oo8ymnZjehQLKb-tJvSHg3UsX8fWHY&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AbQSt7wdiGk5LYCzB3JYahxqsyIJMZeLks5sLUz7gaJpZM4OQIbC&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=_yMTaNh6REuSNjXkVnyyasYyxYJXCEVZL5lJGMxMFyI&s=ywRqbv-hWJqjXo7mGcZ8VDmeo70Z0GvfSnebshkRi6c&e= .

karlcz commented 7 years ago

Unfortunately, I don't understand how that existing segments file was generated and cannot see a way to recover it. I think you'll just have to segment the image region over again.

Not only are the out-of-range coordinates odd, but the included "raw core" and "raw hollow" measurements do not correspond to measurements obtained when analyzing the source image. I even tried a larger slice region that should produce a superset of the measurements in any segment file generated from that same image.

If this was one of the first ones performed while testing the new launcher+viewer integration, we might chalk it up to the bugs we were hashing through in those first days...? If this is a recurring problem, it might indicate a more serious file-handling bug that scrambled up image or result files.

BDemps commented 7 years ago

It's likely that this may have even been the first one that she segmented... Bummer, because Yasmin is no longer in the lab, so this data is likely lost, unless the at-home version of the 2D slicer comes online and we can convinve her to try once more!

On Thu, Jul 6, 2017 at 3:21 PM, Karl Czajkowski notifications@github.com wrote:

Unfortunately, I don't understand how that existing segments file was generated and cannot see a way to recover it. I think you'll just have to segment the image region over again.

Not only are the out-of-range coordinates odd, but the included "raw core" and "raw hollow" measurements do not correspond to measurements obtained when analyzing the source image. I even tried a larger slice region that should produce a superset of the measurements in any segment file generated from that same image.

If this was one of the first ones performed while testing the new launcher+viewer integration, we might chalk it up to the bugs we were hashing through in those first days...? If this is a recurring problem, it might indicate a more serious file-handling bug that scrambled up image or result files.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_informatics-2Disi-2Dedu_synspy_issues_27-23issuecomment-2D313535306&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=-fgSXZTu1LH5U9e3SuZIrdNC8Iji-Evz5m5iZRpNLjA&s=LYmo17Tl0pcBQ_5PbO1xXrAF4FK9TQe-5VTd3oJU_GI&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AbQStyc-5F4v9tHS5f8Wh2dvL8RhxE7RwWks5sLV36gaJpZM4OQIbC&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=-fgSXZTu1LH5U9e3SuZIrdNC8Iji-Evz5m5iZRpNLjA&s=5ZGAmmK8iYcDox3nwOWCXWfLVxRMgcZVg1XAR7US8IY&e= .

-- William Dempsey, Ph.D. Postdoctoral Scholar Molecular and Computational Biology Dana and David Dornsife College of Letters, Arts and Sciences University of Southern California wdempsey@usc.edu Lab #: 213-821-1818