Exe version stuck at simulated OTF processing

[cleterrier]

Hi,

I'm trying to process a 3D-SIM acquisition from our Nikon N-SIM S microscope to test open3DSIM. I have reorganized the acquired data (actin in a COS cell) as a stack (1024x1024 pixels XY planes, 5 phases, Z=40 planes, 3 orientations) available here:
https://filesender.renater.fr/?s=download&token=0a764d54-f7ce-43dd-9854-02fc561c58c4

I'm using Open3DSIM exe method with the 2018a Matlab runtime. I can read my stack by clicking on the "Read" button, and fill all required information in the parameters as shown here:

However, when clicking on "Process" to generate the simulated OTF, the program hangs (I let it run for more than an hour with no result, still on Status: Processing). The logFile.txt in the exe folder end up containing the following lines:

In function deconvlucy, size of the PSF must not exceed the image size in any nonsingleton dimension.
parse_inputs at 286
deconvlucy at 105
find_illumination_pattern at 24
process_data at 54
app1.Process at 228
AppManagementService.tryCallback at 283
@(source,event)tryCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event) at 0 

Any idea of what goes wrong and how I could manage to go further into processing this data?

[Cao-ruijie]

Dear： Thank you for your attention for our platform， i am downloading your data and will reply soon. Because our program is based on OMX，so i infer it may be because of the input format. I will find the bug to reply to you soon and our platform will continue to be improved to be compatible to other commercial system. Thank you！ 曹睿杰 ***@***.***

…

---- Replied Message ---- From Christophe ***@***.***>Date 12/23/2022 07:35To ***@***.***>Cc ***@***.***>Subject [Cao-ruijie/Open3DSIM] Exe version stuck at simulated ORF processing (Issue #1) Hi, I'm trying to process a 3D-SIM acquisition from our Nikon N-SIM S microscope to test open3DSIM. I have reorganized the acquired data (actin in a COS cell) as a stack (1024x1024 pixels XY planes, 5 phases, Z=40 planes, 3 orientations) available here: https://filesender.renater.fr/?s=download&token=0a764d54-f7ce-43dd-9854-02fc561c58c4 I'm using Open3DSIM exe method with the 2018a Matlab runtime. I can read my stack by clicking on the "Read" button, and fill all required information in the parameters as shown here: However, when clicking on "Process" to generate the simulated OTF, the program hangs (I let it run for more than an hour with no result, still on Status: Processing). The logFile.txt in the exe folder end up containing the following lines: In function deconvlucy, size of the PSF must not exceed the image size in any nonsingleton dimension. parse_inputs at 286 deconvlucy at 105 find_illumination_pattern at 24 process_data at 54 app1.Process at 228 AppManagementService.tryCallback at 283 @(source,event)tryCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event) at 0 Any idea of what goes wrong and how I could manage to go further into processing this data? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Cao-ruijie]

Dear Dr. Letterier, I have successfully run your data, and I reply to you immediately. Please receive the Reply.zip file. We develop Open-3DSIM based on GE | OMX system, so its input format may be different from N-SIM. But the principle of reconstruction is the same. Open-3DSIM use the data format of: phase-depth-channel-time-angle. So I write a code (NSIM_format.m in directory Convert) to convert your data to the input of Open-3DSIM and successfully run it without change in other reconstruction code. Not only that, I have provided the converted original data (including large images “Actin_488_large.tif” and cropped small images “Actin_488_small.tif”, large images are suitable to the server side, and small images are applicable to personal computers) for your testing. Please use our updated Exe version to run it (We have corrected a small bug. The Updated “Open_3DSIMM_v1.exe” can be seen in the email and will update to Github soon). The parameter is the same as you provided. Note that the edgetaper choose 0. Using the cropped small images, the processing time is about 2 min, and the filter process will take about 0.5 min. I have run it and provide the reconstructed results in the email as “Open_3DSIM_big.tif” and “Open_3DSIM_small.tif” for your reference. And run its polarized distribution image as “pSIM_big.tif”. The parallelism between actin orientation and polarization proves the function to interpret the polarization. Despite it did not do intensity calibration. For sincere requests, we hope to constantly improve Open-3DSIM to apply to different commercial SIM systems. Can you provide us with the original N-SIM version data, and authorize us to publish it on github as test data? We will thank you and your organization in Github, figshare and the papers to be published. Thank you! I look forward to hearing from you. From: Christophe Leterrier ***@***.***> Date: 2022-12-23 07:35:00 To: Cao-ruijie/Open3DSIM ***@***.***> Cc: Subscribed ***@***.***> Subject: [Cao-ruijie/Open3DSIM] Exe version stuck at simulated ORF processing (Issue #1) Hi, I'm trying to process a 3D-SIM acquisition from our Nikon N-SIM S microscope to test open3DSIM. I have reorganized the acquired data (actin in a COS cell) as a stack (1024x1024 pixels XY planes, 5 phases, Z=40 planes, 3 orientations) available here: https://filesender.renater.fr/?s=download&token=0a764d54-f7ce-43dd-9854-02fc561c58c4 I'm using Open3DSIM exe method with the 2018a Matlab runtime. I can read my stack by clicking on the "Read" button, and fill all required information in the parameters as shown here: However, when clicking on "Process" to generate the simulated OTF, the program hangs (I let it run for more than an hour with no result, still on Status: Processing). The logFile.txt in the exe folder end up containing the following lines: In function deconvlucy, size of the PSF must not exceed the image size in any nonsingleton dimension. parse_inputs at 286 deconvlucy at 105 find_illumination_pattern at 24 process_data at 54 app1.Process at 228 AppManagementService.tryCallback at 283 @(source,event)tryCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event) at 0 Any idea of what goes wrong and how I could manage to go further into processing this data? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> 从网易企业邮箱发来的云附件 Actin_488_large.tif 140.33M | 过期时间：2023年1月7日 13:25 下载 Open_3DSIM_v1.exe 67.83M | 过期时间：2023年1月7日 13:26 下载 pSIM_big.tif 123.17M | 过期时间：2023年1月7日 13:28 下载 从网易企业邮箱发来的云附件 Reply.zip 268.18M | 过期时间：2023年1月7日 13:40 下载

[Cao-ruijie]

Dear professor： From: Christophe Leterrier ***@***.***> Date: 2022-12-23 07:35:00 To: Cao-ruijie/Open3DSIM ***@***.***> Cc: Subscribed ***@***.***> Subject: [Cao-ruijie/Open3DSIM] Exe version stuck at simulated ORF processing (Issue #1) Hi, I'm trying to process a 3D-SIM acquisition from our Nikon N-SIM S microscope to test open3DSIM. I have reorganized the acquired data (actin in a COS cell) as a stack (1024x1024 pixels XY planes, 5 phases, Z=40 planes, 3 orientations) available here: https://filesender.renater.fr/?s=download&token=0a764d54-f7ce-43dd-9854-02fc561c58c4 I'm using Open3DSIM exe method with the 2018a Matlab runtime. I can read my stack by clicking on the "Read" button, and fill all required information in the parameters as shown here: However, when clicking on "Process" to generate the simulated OTF, the program hangs (I let it run for more than an hour with no result, still on Status: Processing). The logFile.txt in the exe folder end up containing the following lines: In function deconvlucy, size of the PSF must not exceed the image size in any nonsingleton dimension. parse_inputs at 286 deconvlucy at 105 find_illumination_pattern at 24 process_data at 54 app1.Process at 228 AppManagementService.tryCallback at 283 @(source,event)tryCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event) at 0 Any idea of what goes wrong and how I could manage to go further into processing this data? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>