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Welcome to My Google Summer of Code 2021 Blog

GSOC project title - ImageJ: Input/Out Workflows for Active Segmentation Platform

GSOC project description :

ImageJ is extensively used in major areas of biological and material sciences. Previously developed active segmentation platform as a plugin for ImageJ incorporate Weka toolbox-based statistical machine learning algorithms as well as deep learning techniques for trainable image segmentation. The end goal of the active segmentation platform for ImageJ is to provide researchers an extensible toolbox enabling them to select custom filters and machine learning algorithms for their research. Especially previously developed semantic segmentation-based techniques are currently in the process of integrating with ImageJ under the Active Segmentation plugin. These techniques are especially based on deep learning algorithms which are state-of-the-art performing procedures for image segmentation.

Under the existing implementation of the active segmentation platform, it only supports users with a limited way to load the ground truth for learning ( at the moment only as of the region on interest format (ROI)). Thus, this reduced the usability of the tool and it urges the users to convert the ground truth to the specific format which is designed to be used within the application. Thus this design is not useful for multiple applications. Therefore the main contributions under this project will be to incorporate several ground-truth formats as image-based in which each pixel uniquely belongs to a particular class, partial ground truth format in which instead of the whole image and several partial boxes in an image or stacks are labeled.

Week-1 (2021 June 07 - 2021 June 11)

1. What have you been doing this week?

  >>> Testing the existing imageJ plugin for active segmentaions for reported issues.
  >>> TIFF based input/output flow for image and groud-truth loadig implemetation.
  >>> GUI bugs testing and enhancement for input flow of the plugin.
 
2. What are you planning to do next week?
  
  >>> Continue on TIFF based input/output flow implemetaion.
  >>> Testing the implemetation.

3. Is anything blocking your progress?

  >>> There exists few issues regarding dependcy configuraion for the imageJ plugin and the mentors are contated and reported the issue.

Week-2 (2021 June 14 - 2021 June 18)

1. What have you been doing this week?

  >>> Fixed issues of project meta information for loading and creating projects for segmentation.
  >>> Fixed issues with Gaussian_K1 filter while loading and applying.
  >>> GUI implemetaion for loading groudtruth from TIFF based groudtruth.
  >>> Fixing issues with testFilter while loading filter.
 
2. What are you planning to do next week?
  
  >>> Pixel based groudtruth loading and dataset creation implemetation.
  >>> Testing the implemetation.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-3 (2021 June 21 - 2021 June 25)

1. What have you been doing this week?

  >>> Pixel based image labels generation for segmentation.
  >>> Studing the LUT procedure (Lookup tables for segementation labeling)
  >>> GUI implemetaion for loading groudtruth from TIFF based groudtruth.
 
2. What are you planning to do next week?
  
  >>> Furter implementation of Pixel based groudtruth loading and dataset creation.
  >>> LUT addon to label identification.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-4 (2021 June 28 - 2021 July 02)

1. What have you been doing this week?

  >>> Implemetation of lookup tables for segmentation masks.
  >>> TIFF images loading.
  >>> GUI implemetaion for lookup tables.
 
2. What are you planning to do next week?
  
  >>> GUI refactoring for multi-label segmentation.
  >>> LUT to enable labels.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-5 (2021 July 05 - 2021 July 09)

1. What have you been doing this week?

  >>> GUI design for mutli-label segementation using lookup tables.
  >>> Histogram based class label identification.

 
2. What are you planning to do next week?
  
  >>> Integration of class labels identifaction and enabling procedure based on user inputs.
  >>> Finalizing the input, output workflow.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-6 (2021 July 12 - 2021 July 16)

1. What have you been doing this week?

  >>> Groud Truth loading and GUI design for overlay.
  >>> Overlay implemetation for groud truth visulaiztion.

 
2. What are you planning to do next week?
  
  >>> Overaly GUI design for user inputs.
  >>> LUT for overaly color changes.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-7 (2021 July 19 - 2021 July 23)

1. What have you been doing this week?

  >>> Overaly implemetation based on number of classes for sgementaton.
  >>> User interaction with overlay.

 
2. What are you planning to do next week?
  
  >>> LUT for overlay.
  >>> Ground truth based training.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-8 (2021 July 26 - 2021 July 30)

1. What have you been doing this week?

  >>> Pixel-based training procedure implementation and dataset creation..
  >>> Implementation of look table based overlay for segmented images.
  >>> UI changes for ground-truth based training.

 
2. What are you planning to do next week?
  
  >>> Optimizations for trainng procedure.
  >>> Updating metadata for groundtruth based training.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-9 (2021 August 2 - 2021 August 6)

1. What have you been doing this week?

  >>> Implementation of updating metadata file using loaded ground-truth.
  >>> Implementation of updating metadata file using training procedure.
  >>> Implementation of loading project from meta data.
  >>> Optimization of training procedure.

 
2. What are you planning to do next week?
  
  >>> Code refactoring.
  >>> Final product submission.

3. Is anything blocking your progress?

  >>> No blockers at the moment.

Week-10 (2021 August 9 - 2021 August 13)

1. What have you been doing this week?

  >>> Code refactoring.
  >>> Final product submission.

 
2. What are you planning to do next week?
  
  >>> Completion of final evaluation.

3. Is anything blocking your progress?

  >>> No blockers at the moment.