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Sami's Developpement #4

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Sami's Developpement #4

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Commits on Apr 18, 2023

  1. Modified path to CONFIG from biom3d.configs.unet_default to biom3d.co… 

    …nfig_default
    @SafarbatiSami
    SafarbatiSami committed Apr 18, 2023
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Commits on Apr 19, 2023

  1. Update README.md 

    Corrections
    @SafarbatiSami
    SafarbatiSami authored Apr 19, 2023
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  2. Merged Preprocessing Tab and Train tab. 

    Modified Display and Style.
    @SafarbatiSami
    SafarbatiSami committed Apr 19, 2023
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  3. Merge branch 'main' of https://github.com/SafarbatiSami/biom3d into main

    @SafarbatiSami
    SafarbatiSami committed Apr 19, 2023
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  4. Added autoConfig in Preprocess_autoconfig() ; 

    Modified Display of Patch size in the Config Frame.
    @SafarbatiSami
    SafarbatiSami committed Apr 19, 2023
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Commits on Apr 21, 2023

  1. Merge remote-tracking branch 'upstream/main' into main

    @SafarbatiSami
    SafarbatiSami committed Apr 21, 2023
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  2. Changed dataType of aug_patch_size, patch_size, num_pools to Lists. 

    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
    SafarbatiSami committed Apr 21, 2023
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Commits on Apr 24, 2023

  1. Correction of train bug

    @SafarbatiSami
    SafarbatiSami committed Apr 24, 2023
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Commits on Apr 27, 2023

  1. Modified Remote interface. 

    Added remote train and autoconfig.
    @SafarbatiSami
    SafarbatiSami committed Apr 27, 2023
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Commits on May 9, 2023

  1. .

    @SafarbatiSami
    SafarbatiSami committed May 9, 2023
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed May 9, 2023
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Commits on May 10, 2023

  1. Added Parameters_return() function to Display config parameters. 

    Added new argument (Remote) to use when on Remote.
    @SafarbatiSami
    SafarbatiSami committed May 10, 2023
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Commits on May 15, 2023

  1. Changes in Remote functioning. 

    Added popup messages.
Redefined dropdown menus.
    @SafarbatiSami
    SafarbatiSami committed May 15, 2023
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Commits on May 16, 2023

  1. Redefined dropdown Menus. 

    Added some popup messages.
Added test to create required folders.
    @SafarbatiSami
    SafarbatiSami committed May 16, 2023
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  2. Added Remote parameter. 

    Added Parameters return function.
    @SafarbatiSami
    SafarbatiSami committed May 16, 2023
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  3. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed May 16, 2023
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Commits on Jun 2, 2023

  1. added a popup message

    @SafarbatiSami
    SafarbatiSami committed Jun 2, 2023
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Jun 2, 2023
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  3. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Jun 2, 2023
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Commits on Jun 5, 2023

  1. Added fg_dir parameter

    @SafarbatiSami
    SafarbatiSami committed Jun 5, 2023
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Jun 5, 2023
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  3. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Jun 5, 2023
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Commits on Jun 6, 2023

  1. modified preprocess for remote

    @SafarbatiSami
    SafarbatiSami committed Jun 6, 2023
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  2. correction for folder selection

    @SafarbatiSami
    SafarbatiSami committed Jun 6, 2023
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Commits on Jun 7, 2023

  1. Changes for window size

    @SafarbatiSami
    SafarbatiSami committed Jun 7, 2023
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  2. correction for config path bug

    @SafarbatiSami
    SafarbatiSami committed Jun 7, 2023
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  3. train bugfix

    @SafarbatiSami
    SafarbatiSami committed Jun 7, 2023
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  4. number of classes bugfix

    @SafarbatiSami
    SafarbatiSami committed Jun 7, 2023
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Commits on Jun 8, 2023

  1. Changed save dir for configs

    @SafarbatiSami
    SafarbatiSami committed Jun 8, 2023
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  2. changed save dir for configs

    @SafarbatiSami
    SafarbatiSami committed Jun 8, 2023
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Commits on Jun 9, 2023

  1. Bugfix remote cfg load/save

    @SafarbatiSami
    SafarbatiSami committed Jun 9, 2023
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Commits on Jun 16, 2023

  1. File to generate the executbale file

    @SafarbatiSami
    SafarbatiSami committed Jun 16, 2023
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  2. Download prediction bugfix

    @SafarbatiSami
    SafarbatiSami committed Jun 16, 2023
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  3. correction popupmsg

    @SafarbatiSami
    SafarbatiSami committed Jun 16, 2023
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  4. Restricted access for local interface while using an executable

    @SafarbatiSami
    SafarbatiSami committed Jun 16, 2023
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Commits on Jun 19, 2023

  1. Modified Button positions

    @SafarbatiSami
    SafarbatiSami committed Jun 19, 2023
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  2. Script to deploy an executable file for User interface

    @SafarbatiSami
    SafarbatiSami committed Jun 19, 2023
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Commits on Jun 20, 2023

  1. Correction for UI

    @SafarbatiSami
    SafarbatiSami committed Jun 20, 2023
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  2. Added Home button, modified positions for config parameters

    @SafarbatiSami
    SafarbatiSami committed Jun 20, 2023
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  3. Corrections for Gui

    @SafarbatiSami
    SafarbatiSami committed Jun 20, 2023
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  4. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
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    SafarbatiSami committed Jun 20, 2023
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Commits on Jun 21, 2023

  1. changed the way to get auto config results

    @SafarbatiSami
    SafarbatiSami committed Jun 21, 2023
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  2. Code Cleaning

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    SafarbatiSami committed Jun 21, 2023
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Commits on Jun 22, 2023

  1. Module to upload predictions in OMERO

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    SafarbatiSami committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. improved Uploader

    @SafarbatiSami
    SafarbatiSami committed Jun 23, 2023
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  2. Added option to send prediction to OMERO

    @SafarbatiSami
    SafarbatiSami committed Jun 23, 2023
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  3. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Jun 23, 2023
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Commits on Jul 3, 2023

  1. improve Omero ulpoad

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    SafarbatiSami committed Jul 3, 2023
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Commits on Jul 5, 2023

  1. Added loop to do all sub folders

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    SafarbatiSami committed Jul 5, 2023
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Commits on Jul 20, 2023

  1. update

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    SafarbatiSami committed Jul 20, 2023
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Commits on Jul 25, 2023

  1. Removed CLI connection.

    @SafarbatiSami
    SafarbatiSami committed Jul 25, 2023
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  2. Updated Gui

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    SafarbatiSami committed Jul 25, 2023
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  3. update

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    SafarbatiSami committed Jul 25, 2023
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Commits on Jul 26, 2023

  1. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Jul 26, 2023
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Jul 26, 2023
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  3. Added project output id for omero

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    SafarbatiSami committed Jul 26, 2023
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Commits on Aug 7, 2023

  1. Added venv activation while using remote

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    SafarbatiSami committed Aug 7, 2023
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Commits on Aug 8, 2023

  1. train loss function plot (still working on it)

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    SafarbatiSami committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. Added training curves

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    SafarbatiSami committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. updated learning curves

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    SafarbatiSami committed Aug 10, 2023
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  2. update

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    SafarbatiSami committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. Correction for leaning curves

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    SafarbatiSami committed Aug 11, 2023
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Commits on Aug 14, 2023

  1. changes in buttons size

    @SafarbatiSami
    SafarbatiSami committed Aug 14, 2023
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Aug 14, 2023
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  3. Update for GUI

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    SafarbatiSami committed Aug 14, 2023
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Commits on Aug 16, 2023

  1. update gui

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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Aug 16, 2023
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  3. blitz bugfix

    @SafarbatiSami
    SafarbatiSami committed Aug 16, 2023
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  4. update gui

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    SafarbatiSami committed Aug 16, 2023
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  5. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Aug 17, 2023
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  2. Revert "Merge branch 'main' of https://github.com/GuillaumeMougeot/bi… 

    …om3d into main"

This reverts commit 745a294, reversing
changes made to 7da89c2.
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Commits on Aug 18, 2023

  1. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Aug 18, 2023
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  2. dataset update bugfix

    @SafarbatiSami
    SafarbatiSami committed Aug 18, 2023
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  3. Final GUI (maybe)

    @SafarbatiSami
    SafarbatiSami committed Aug 18, 2023
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  4. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Aug 18, 2023
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  5. number of classes bugfix

    @SafarbatiSami
    SafarbatiSami committed Aug 18, 2023
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  6. plot bugfix

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    SafarbatiSami committed Aug 18, 2023
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Commits on Sep 8, 2023

  1. Learning curve Bugfix

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    SafarbatiSami committed Sep 8, 2023
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  2. Merge branch 'main' of https://github.com/SafarbatiSami/biom3d into main

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Commits on Sep 11, 2023

  1. Added Objects filtering for prediction in GUI

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    SafarbatiSami committed Sep 11, 2023
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  2. Learning curves bufix

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    SafarbatiSami committed Sep 11, 2023
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  3. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
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Commits on Sep 13, 2023

  1. Added option to use a config file for training

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    SafarbatiSami committed Sep 13, 2023
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Commits on Sep 15, 2023

  1. Added function descriptions, added option to choose where to store lo… 

    …gs, newline bugfix, load config bugfix
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Commits on Sep 18, 2023

  1. Code Cleaning, removed useless stuff

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Commits on Sep 19, 2023

  1. Added some doc

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    SafarbatiSami committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. Error handling

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    SafarbatiSami committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. Added Ressources computing

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    SafarbatiSami committed Sep 21, 2023
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Commits on Sep 22, 2023

  1. Removed useless imports

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    SafarbatiSami committed Sep 22, 2023
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  2. modified import

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    SafarbatiSami committed Sep 22, 2023
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Commits on Sep 25, 2023

  1. Windows path Bugfix

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    SafarbatiSami committed Sep 25, 2023
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
    @SafarbatiSami
    SafarbatiSami committed Sep 25, 2023
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  3. error handling

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    SafarbatiSami committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. text modification

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    SafarbatiSami committed Sep 26, 2023
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  2. text correction

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    SafarbatiSami committed Sep 26, 2023
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  3. text correction

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    SafarbatiSami committed Sep 26, 2023
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  4. text correction

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    SafarbatiSami committed Sep 26, 2023
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Commits on Oct 2, 2023

  1. Added Fine tuning in local

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    SafarbatiSami committed Oct 2, 2023
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Commits on Oct 3, 2023

  1. Added 3 display modes, added fine-tuning in local & remote

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    SafarbatiSami committed Oct 3, 2023
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Commits on Oct 4, 2023

  1. Remote fine tuning update

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    SafarbatiSami committed Oct 4, 2023
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Commits on Oct 10, 2023

  1. classes bugfix, path bugfix

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    SafarbatiSami committed Oct 10, 2023
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
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    SafarbatiSami committed Oct 10, 2023
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Commits on Oct 30, 2023

  1. Corrections for Local Path

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    SafarbatiSami committed Oct 30, 2023
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Commits on Dec 19, 2023

  1. updated gui

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    SafarbatiSami committed Dec 19, 2023
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Commits on Dec 20, 2023

  1. Documentation( en cours)

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    SafarbatiSami committed Dec 20, 2023
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  2. Trainers documentation

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    SafarbatiSami committed Dec 20, 2023
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  3. Predictors Documentation

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    SafarbatiSami committed Dec 20, 2023
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  4. Semseg_torchio Documentation

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    SafarbatiSami committed Dec 20, 2023
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  5. Semseg_patch_fast Documentation

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    SafarbatiSami committed Dec 20, 2023
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  6. Semseg_Batchgen Documentation

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    SafarbatiSami committed Dec 20, 2023
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Commits on Dec 21, 2023

  1. Added browse button in splash screen

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    SafarbatiSami committed Dec 21, 2023
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  2. Added Biom3d logo to the Gui

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    SafarbatiSami committed Dec 21, 2023
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Commits on Mar 21, 2024

  1. Adapted preprocessing for 2d images

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    SafarbatiSami committed Mar 21, 2024
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  2. added doc

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    SafarbatiSami committed Mar 21, 2024
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  3. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o main
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    SafarbatiSami committed Mar 21, 2024
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Commits on Mar 27, 2024

  1. version 0.0.38

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    GuillaumeMougeot committed Mar 27, 2024
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Commits on Apr 12, 2024

  1. implementation of 2d segmentation

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    SafarbatiSami committed Apr 12, 2024
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  2. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o 2D_Segmentation
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    SafarbatiSami committed Apr 12, 2024
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Commits on Apr 26, 2024

  1. Bufix arborescence upload, added attachement file to omero upload

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    SafarbatiSami committed Apr 26, 2024
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  2. Inverted Z & T bugfix

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    SafarbatiSami committed Apr 26, 2024
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Commits on Jun 13, 2024

  1. Corrections for PR

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    SafarbatiSami committed Jun 13, 2024
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Commits on Jun 17, 2024

  1. corrected is2d to is_2d

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    SafarbatiSami committed Jun 17, 2024
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Commits on Jun 19, 2024

  1. Added Model as upload File in OMERO

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    SafarbatiSami committed Jun 19, 2024
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  2. Data managment after OMERO prediction

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    SafarbatiSami committed Jun 19, 2024
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  3. Module for training with OMERO data

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    SafarbatiSami committed Jun 19, 2024
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  4. Updated GUI ( Omero Training, Omero Pred ...)

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    SafarbatiSami committed Jun 19, 2024
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Commits on Jun 25, 2024

  1. latest tests

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    GuillaumeMougeot committed Jun 25, 2024
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  2. preprocessing - minor fix for 4-dimensional masks

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    GuillaumeMougeot committed Jun 25, 2024
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  3. minor fix on preprocessing

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    GuillaumeMougeot committed Jun 25, 2024
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Commits on Jun 28, 2024

  1. Removed torch version in dependency for Colab.

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    GuillaumeMougeot committed Jun 28, 2024
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  2. updated version in Colab

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    GuillaumeMougeot committed Jun 28, 2024
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Commits on Jul 5, 2024

  1. added efficientUnet

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    GuillaumeMougeot committed Jul 5, 2024
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  2. added efficientUnet in register

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    GuillaumeMougeot committed Jul 5, 2024
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  3. removed useless comments

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    GuillaumeMougeot committed Jul 5, 2024
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Commits on Jul 8, 2024

  1. updated colab for torchio

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    GuillaumeMougeot committed Jul 8, 2024
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  2. Omero connection with session id

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    SafarbatiSami committed Jul 8, 2024
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  3. Merge branch 'main' of https://github.com/GuillaumeMougeot/biom3d int… 

    …o 2D_Segmentation
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    SafarbatiSami committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. updated Omero preprocess_train ( now uploads training images)

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    SafarbatiSami committed Jul 9, 2024
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  2. Added Omero upload after training in GUI

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    SafarbatiSami committed Jul 9, 2024
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Commits on Jul 11, 2024

  1. num_worker to 1

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    SafarbatiSami committed Jul 11, 2024
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Commits on Jul 15, 2024

  1. Changed num_workers to 8

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    SafarbatiSami authored Jul 15, 2024
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Commits on Jul 17, 2024

  1. removed try catch for omero_uploader

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    SafarbatiSami committed Jul 17, 2024
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  2. changed num of workers back to 6

    @SafarbatiSami
    SafarbatiSami authored Jul 17, 2024
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  3. removed useless import

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    SafarbatiSami committed Jul 17, 2024
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  4. Merge branch '2D_Segmentation' of https://github.com/SafarbatiSami/bi… 

    …om3d into 2D_Segmentation
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    SafarbatiSami committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. Adapted omero uploader to use session id

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    SafarbatiSami committed Jul 18, 2024
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Commits on Jul 22, 2024

  1. Added File annotation download

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    SafarbatiSami committed Jul 22, 2024
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  2. Adapted omero uploader for omero_preprocess_train

    @SafarbatiSami
    SafarbatiSami committed Jul 22, 2024
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  3. Added learning curves plot, Added autoconfig, train

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    SafarbatiSami committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. Correction for omero session bug

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    SafarbatiSami committed Jul 23, 2024
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Commits on Jul 25, 2024

  1. Added prediction for omero_preprocess_train

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    SafarbatiSami committed Jul 25, 2024
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