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Corrections for last PR #6

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@SafarbatiSami SafarbatiSami commented Jul 8, 2024 •
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⚠️ Modify PR for DEV branch not MAIN ⚠️

  • Corrections for the last PR
  • Added possibility to use data from Omero for training (the new model is stored in omero as file attachment)
  • Get session id if already connected to Omero
  • Data management after predictions
  • Updated GUI

SafarbatiSami and others added 30 commits April 18, 2023 12:32
@SafarbatiSami
Modified path to CONFIG from biom3d.configs.unet_default to biom3d.co…
05bb833 
…nfig_default
@SafarbatiSami
Update README.md
6328037 
Corrections
@SafarbatiSami
Merged Preprocessing Tab and Train tab.
62c716b 
Modified Display and Style.
@SafarbatiSami
Merge branch 'main' of https://github.com/SafarbatiSami/biom3d into main
14309eb
@SafarbatiSami
Added autoConfig in Preprocess_autoconfig() ;
5423e0e 
Modified Display of Patch size in the Config Frame.
@SafarbatiSami
Merge remote-tracking branch 'upstream/main' into main
2259dac
@SafarbatiSami
Changed dataType of aug_patch_size, patch_size, num_pools to Lists.
73a9e13 
Modified inputs of patch size , augmentation patch size and number of pool .

Added function to preprocess, autoconfig, save config, print path to config, and update text boxes after run.

Modified button colors and size .
@SafarbatiSami
Correction of train bug
e4d69ab
@SafarbatiSami
Modified Remote interface.
54d0686 
Added remote train and autoconfig.
@SafarbatiSami
.
4d2707b
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
06e41ad 
…o main
@SafarbatiSami
Added Parameters_return() function to Display config parameters.
a627343 
Added new argument (Remote) to use when on Remote.
@SafarbatiSami
Changes in Remote functioning.
98141f8 
Added popup messages.
Redefined dropdown menus.
@SafarbatiSami
Redefined dropdown Menus.
8c99ae7 
Added some popup messages.
Added test to create required folders.
@SafarbatiSami
Added Remote parameter.
46cade7 
Added Parameters return function.
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
536b7f9 
…o main
@SafarbatiSami
added a popup message
7ffa3ce
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
308e464 
…o main
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
abc363d 
…o main
@SafarbatiSami
Added fg_dir parameter
2a73681
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
9cc40d3 
…o main
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
295e86d 
…o main
@SafarbatiSami
modified preprocess for remote
a41fde3
@SafarbatiSami
correction for folder selection
b4417de
@SafarbatiSami
Changes for window size
954f64d
@SafarbatiSami
correction for config path bug
9734cb4
@SafarbatiSami
train bugfix
9cb0d7a
@SafarbatiSami
number of classes bugfix
49f8580
@SafarbatiSami
Changed save dir for configs
b90174e
@SafarbatiSami
changed save dir for configs
0c4cfba
SafarbatiSami and others added 30 commits December 21, 2023 11:32
@SafarbatiSami
Added Biom3d logo to the Gui
e5b5255
@SafarbatiSami
Adapted preprocessing for 2d images
44302bf
@SafarbatiSami
added doc
78269d2
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
ee3bf77 
…o main
@SafarbatiSami
implementation of 2d segmentation
cedc40b
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
d56cc6d 
…o 2D_Segmentation
@SafarbatiSami
Bufix arborescence upload, added attachement file to omero upload
aec59e1
@SafarbatiSami
Inverted Z & T bugfix
095650f
@SafarbatiSami
Corrections for PR
09f77e6
@SafarbatiSami
corrected is2d to is_2d
409d7cc
@SafarbatiSami
Added Model as upload File in OMERO
733c482
@SafarbatiSami
Data managment after OMERO prediction
2ff92b2
@SafarbatiSami
Module for training with OMERO data
9119cba
@SafarbatiSami
Updated GUI ( Omero Training, Omero Pred ...)
a14f26d
@SafarbatiSami
Omero connection with session id
76869bd
@SafarbatiSami
Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int…
3bd5b28 
…o 2D_Segmentation
@SafarbatiSami
updated Omero preprocess_train ( now uploads training images)
84ddbb5
@SafarbatiSami
Added Omero upload after training in GUI
05b6ece
@SafarbatiSami
num_worker to 1
6e11ec3
@SafarbatiSami
Changed num_workers to 8
c488dce
@SafarbatiSami
removed try catch for omero_uploader
bf1fa04
@SafarbatiSami
changed num of workers back to 6
1edd81f
@SafarbatiSami
removed useless import
c26e351
@SafarbatiSami
Merge branch '2D_Segmentation' of https://github.com/SafarbatiSami/bi…
8884ef9 
…om3d into 2D_Segmentation
@SafarbatiSami
Adapted omero uploader to use session id
cacc806
@SafarbatiSami
Added File annotation download
4e052ed
@SafarbatiSami
Adapted omero uploader for omero_preprocess_train
ed9ef6d
@SafarbatiSami
Added learning curves plot, Added autoconfig, train
80c1b5e
@SafarbatiSami
Correction for omero session bug
295b099
@SafarbatiSami
Added prediction for omero_preprocess_train
e48bc68
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