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isensee (Fabian Isensee)
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Aug 1 2016, 12:10 PM (260 w, 5 d)

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Jun 4 2021

isensee updated the task description for T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
Jun 4 2021, 12:19 PM · MITK (v2021.10)
isensee added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

As it is an inexpensive operation my first guess would be an issue related to the amount of used memory. For example, the image above eats 3,5 GB, Activating the interpolation already triples it. Confirming adds at least another 3,5 GB. That could also explain why it is so slow (swapping). But at this point it is just a first assumption. On a 16 GB Windows machine I was able to complete the interpolation without crash but it took a while.

Jun 4 2021, 12:17 PM · MITK (v2021.10)
isensee created T28522: Segmentations are drawn differently depending on whether the segmentation tool is open or not.
Jun 4 2021, 12:15 PM · MITK
isensee created T28521: multilabel segmentation add switch to disable contour.
Jun 4 2021, 12:12 PM · MITK

Jun 2 2021

isensee updated subscribers of T28491: Slice interpolation 'confirm for all slices' not working for large images.

@kislinsk I know you have plenty of things to do, but this bug (along with T28516) is a blocker at the moment. I would like to recommend MITK as an annotation tool for our collaborators but cannot do that as along as the slice interpolation does not work (fast enough, T28516) for large images :-)

Jun 2 2021, 9:24 AM · MITK (v2021.10)
isensee created T28516: 2D slice interpolation should use multiprocessing.
Jun 2 2021, 9:22 AM · MITK (v2021.10)

Jun 1 2021

isensee added a comment to T28422: Multilabel color map does not produce unique colors.

@kislinsk sorry for the late reply. I am not using the convert to segmentation functionality because it draws contours by default and that is annoying because it obstructs too much from the image. Multilabel color map does exactly the right thing, is easy to use and does not require and additional mouse clicks. It is just more convenient :-)

Jun 1 2021, 5:02 PM · MITK (v2021.10)

May 25 2021

isensee updated the task description for T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
May 25 2021, 11:14 AM · MITK (v2021.10)
isensee created T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
May 25 2021, 11:13 AM · MITK (v2021.10)

May 20 2021

isensee added a comment to T28493: Multilabel color map colors are not very nice.
import numpy as np
import colorsys
from skimage import io
May 20 2021, 9:43 AM · MITK
isensee created T28493: Multilabel color map colors are not very nice.
May 20 2021, 9:19 AM · MITK

May 19 2021

isensee updated the task description for T28491: Slice interpolation 'confirm for all slices' not working for large images.
May 19 2021, 10:12 AM · MITK (v2021.10)
isensee created T28491: Slice interpolation 'confirm for all slices' not working for large images.
May 19 2021, 8:11 AM · MITK (v2021.10)
isensee updated the task description for T28490: Segmentation plugin: "new" segmentation should not run reinit!.
May 19 2021, 7:51 AM · Cleared, MITK (v2021.10)
isensee created T28490: Segmentation plugin: "new" segmentation should not run reinit!.
May 19 2021, 7:51 AM · Cleared, MITK (v2021.10)
isensee created T28489: int64 not supported.
May 19 2021, 7:40 AM · MITK

Apr 7 2021

isensee added a comment to T28437: 3D region growing may have issues when the seed point is on a pixel with value 0.

Link to data: https://sas.desy.de/index.php/s/JQgZT5xLCk6RXDg

Apr 7 2021, 1:32 PM · MITK (v2021.10)
isensee created T28437: 3D region growing may have issues when the seed point is on a pixel with value 0.
Apr 7 2021, 11:59 AM · MITK (v2021.10)

Mar 29 2021

isensee updated the task description for T28422: Multilabel color map does not produce unique colors.
Mar 29 2021, 1:20 PM · MITK (v2021.10)
isensee updated the task description for T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel'.
Mar 29 2021, 1:20 PM · MITK (v2021.10)
isensee updated the task description for T28422: Multilabel color map does not produce unique colors.
Mar 29 2021, 1:17 PM · MITK (v2021.10)
isensee created T28422: Multilabel color map does not produce unique colors.
Mar 29 2021, 1:17 PM · MITK (v2021.10)
isensee renamed T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel' from Use whole image grey value must always be executed when switching colormap to to Use whole image grey value must always be executed when switching colormap to 'Multilabel'.
Mar 29 2021, 1:07 PM · MITK (v2021.10)
isensee created T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel'.
Mar 29 2021, 12:59 PM · MITK (v2021.10)

Mar 26 2021

isensee created T28419: better rounding and cleaner overview table.
Mar 26 2021, 11:53 AM · LSF GPU Cluster Monitoring

Mar 23 2021

isensee added a member for Deep Learning: s522r.
Mar 23 2021, 2:51 PM
isensee added a member for MIC: s522r.
Mar 23 2021, 2:51 PM
isensee moved T28396: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05] from Backlog to Open on the LSF GPU Cluster Monitoring board.
Mar 23 2021, 2:15 PM · LSF GPU Cluster Monitoring
isensee moved T28397: display horizontal line in GPU memory plot to show requested GPU memory from Backlog to Open on the LSF GPU Cluster Monitoring board.
Mar 23 2021, 2:15 PM · LSF GPU Cluster Monitoring
isensee moved T28398: somehow use the run time reported by lsf instead of my own from Backlog to Open on the LSF GPU Cluster Monitoring board.
Mar 23 2021, 2:15 PM · LSF GPU Cluster Monitoring
isensee claimed T28398: somehow use the run time reported by lsf instead of my own.
Mar 23 2021, 2:14 PM · LSF GPU Cluster Monitoring
isensee created T28398: somehow use the run time reported by lsf instead of my own.
Mar 23 2021, 2:14 PM · LSF GPU Cluster Monitoring
isensee claimed T28397: display horizontal line in GPU memory plot to show requested GPU memory.
Mar 23 2021, 2:12 PM · LSF GPU Cluster Monitoring
isensee created T28397: display horizontal line in GPU memory plot to show requested GPU memory.
Mar 23 2021, 2:12 PM · LSF GPU Cluster Monitoring
isensee renamed T28396: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05] from Todo Fabian: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05] to scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05].
Mar 23 2021, 2:12 PM · LSF GPU Cluster Monitoring
isensee created T28396: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05].
Mar 23 2021, 2:11 PM · LSF GPU Cluster Monitoring

Feb 18 2021

isensee added a member for Deep Learning: l374d.
Feb 18 2021, 3:06 PM

Oct 29 2020

isensee added a member for Deep Learning: full.
Oct 29 2020, 2:37 PM