Empty 'valid_seg' after running 'neuron_segmentation_module_alter(...)'

[JAMoreno-Larios]

Hello,

I am trying to run MesoLF with my own data. The microscope setup is a traditional LFM and my configuration parameters are the following:

SIin.indir = '/home/jose/path/to/folder/20220614_mouse2_exp2/';
SIin.outdir = [workdir filesep() 'mesolf_mouse2_frames1to2400'];
SIin.frames_start = 1;
SIin.frames_step = 1;
SIin.frames_end = 1200;
SIin.frameRate = 20;
SIin.frames_average = false;
SIin.frames_x_offset = 1040.0;
SIin.frames_y_offset = 1036.0;
SIin.frames_dx = 31.2;
SIin.frames_crop_border_microlenses = [1 1 1 1];
SIin.mask_file = false;  % don't mask out anything, all is valid
SIin.patch_mode = 'carpet';
SIin.n_patches = [1 1];  % 1x1
SIin.psffile = fullfile(workdir, 'PSFmatrix_M10NA0.5MLPitch125fml1250from-200to0zspacing20Nnum15lambda520n1.0.mat');
SIin.gpu_ids = 1;  % select high-performance GPU here; indices start at 1 (so, add one to the gpu indices reported by nvidia-smi, which start at 0)
SIin.filt_method = 'cnn';
% Added by Jose
SIin.reg_flag = false; % Registration
SIin.reg_bin_width = 100;
SIin.valid_recon_range = 11; % Requires integer type
SIin.neuron_lateral_size = 10; %

I am using a 10x microscope with an NA of 0.5, my microlens array pitch is 125 [um], its focal length is 1250 [um], spanning from -200 to 0 [um], resampling to 15 pixels/lenslet, with a carrier wavelength of 520 [nm] and assuming n=1.

In this link you will find the files generated from mesolf.m up to the point of failure. I would appreciate any insights on how to solve this issue.

[nobias]

Hi José, thank you for your detailed bug reports and the pull request. I'll definitely look into this and get back to you as soon as I can. Please allow a few days.

[JAMoreno-Larios]

Hi José, thank you for your detailed bug reports and the pull request. I'll definitely look into this and get back to you as soon as I can. Please allow a few days.

Hi Tobias, I hope you're doing well.
I was wondering if you had any chance to check out the bug report. Thank you!

[nobias]

Hi José! Sorry for the late reply. Could you send me a link to an example of your data? I’ll keep it confidential. Feel free to email it to me at [email protected]