Dl focus track#142

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rthiermann wants to merge 235 commits intojunlabucsd:devfrom

jwschroeder3:dl_focus_track

Commits on Dec 24, 2018

Commits on Jan 7, 2019

debug
jwschroeder3
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Commits on Jan 8, 2019

param info
jtsauls
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Commits on Jan 10, 2019

infinity to avoid future bugs
jtsauls
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Commits on Jan 11, 2019

formatting
jtsauls
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Commits on Jan 14, 2019

Added channel picking CNN
jwschroeder3
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More functionality for channel picking CNN.
jwschroeder3
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Removed unnecessary weights files
jwschroeder3
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Updated params_Unet.yaml in yaml_templates to support CNN-based channel picking.
jwschroeder3
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Updated interactive and static plotting utilities to support CNN-based channel picking.
jwschroeder3
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Commits on Jan 15, 2019

Changed aux to misc for windows compatability
jwschroeder3
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Commits on Jan 16, 2019

added mm3_metamorphToTIFF.py
jwschroeder3
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revert back to aux instead of misc
jwschroeder3
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Commits on Jan 18, 2019

Added multi-fov support and HDF5 support for Unet
jwschroeder3
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Merge pull request #89 from jwschroeder3/unet
jwschroeder3
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Commits on Jan 21, 2019

Fixed bug in writing of specs.yaml file.
jwschroeder3
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Fixed bug in writing of specs.yaml file.
jwschroeder3
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Merge pull request #90 from jwschroeder3/unet
jwschroeder3
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Commits on Jan 22, 2019

debugged minor issue with mm3_Compile.py when using Unet
jwschroeder3
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Merge pull request #91 from jwschroeder3/unet
jwschroeder3
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minor change to peak finder
jtsauls
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fixed conflicts
jtsauls
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Commits on Jan 23, 2019

formatting
jtsauls
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Commits on Jan 24, 2019

added appropriate yaml_template file
jwschroeder3
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Merge pull request #92 from jwschroeder3/unet
jwschroeder3
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Commits on Jan 25, 2019

Commits on Jan 27, 2019

changed logic for what to do in channel picker re identifying channels
jtsauls
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Commits on Feb 4, 2019

Commits on Feb 7, 2019

Commits on Feb 12, 2019

parameter directions
jtsauls
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Commits on Feb 14, 2019

change prediction output to max to 100 rather than 255
jtsauls
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Commits on Feb 18, 2019

Commits on Feb 19, 2019

Added functionality for CNN-aided training data generation.
jwschroeder3
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Merge pull request #96 from jwschroeder3/unet
jwschroeder3
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Commits on Feb 25, 2019

surpress warnings option
jtsauls
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Commits on Feb 28, 2019

untested fix in __data_generation for *self.dim syntax
jtsauls
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debugging CNN channel finding
jtsauls
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format
jtsauls
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Merge pull request #98 from jtsauls/unet
jtsauls
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channel mask file is now yaml. Included support for t_start in compile
jtsauls
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channel mask file is now yaml. Included support for t_start in compile
jtsauls
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time table to .yaml
jtsauls
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Added GUI
jwschroeder3
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resolved conflict
jwschroeder3
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Merge pull request #100 from jwschroeder3/unet
jwschroeder3
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Removed old GUI stuff from mm3_helpers.py
jwschroeder3
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Add t_start to mm3_Compile.py
jwschroeder3
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Merge pull request #101 from jwschroeder3/unet
jwschroeder3
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Commits on Mar 1, 2019

merged in PR #101
jtsauls
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safer parameter loading t_start/t_end
jtsauls
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Fix bug in output file naming for GUI
jwschroeder3
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Merge pull request #102 from jwschroeder3/unet
jwschroeder3
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Fixed major phase image saving bug in GUI
jwschroeder3
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Merge pull request #104 from jwschroeder3/unet
jwschroeder3
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Commits on Mar 2, 2019

cleaning up
jtsauls
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Commits on Mar 3, 2019

numpy floats for new time table when calculating tau
jtsauls
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Commits on Mar 4, 2019

Commits on Mar 5, 2019

Commits on Mar 6, 2019

Commits on Mar 7, 2019

Commits on Mar 11, 2019

foci analysis py3 fixes
jtsauls
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Commits on Mar 12, 2019

Commits on Mar 14, 2019

plotting bug fixes
jtsauls
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Commits on Mar 15, 2019

plot update
jtsauls
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Commits on Mar 26, 2019

Fixed mm3_Compile bug for images with fewer than three imaging channels.
jwschroeder3
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Merge pull request #108 from jwschroeder3/unet
jwschroeder3
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Commits on Mar 29, 2019

plotting
jtsauls
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Commits on Apr 11, 2019

Reworked channel picking to use semantic segmentation of cells
jwschroeder3
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Merge pull request #109 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 12, 2019

Make channel picker with do_seg more efficient
jwschroeder3
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Merge pull request #110 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 16, 2019

Quick bug fix for mm3_Commit.py
jwschroeder3
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Merge pull request #111 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 17, 2019

Initial work on tracking training data gui
jwschroeder3
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Merge pull request #112 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 19, 2019

more tracking gui work
jwschroeder3
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Merge pull request #113 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 23, 2019

Commits on Apr 24, 2019

Plot events from existing tracking data in track GUI
jwschroeder3
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Plot events from existing tracking data in track GUI
jwschroeder3
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Merge pull request #115 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 25, 2019

Yet another tracking gui update
jwschroeder3
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Merge pull request #116 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 26, 2019

Re-code tracking gui to initialize with all frames/cells as qgraphicsitems
jwschroeder3
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Tracking GUI works okay now. Several bugs need worked out, including fov and peak advancing.
jwschroeder3
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Merge pull request #117 from jwschroeder3/unet
jwschroeder3
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Commits on Apr 29, 2019

Fixed bug in advancing trap/fov in tracking gui
jwschroeder3
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Merge pull request #118 from jwschroeder3/unet
jwschroeder3
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track updates
jwschroeder3
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Commits on Apr 30, 2019

Enabled mouse wheel zooming when ctrl is clicked and panning with alt clicked
jwschroeder3
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Merge pull request #120 from jwschroeder3/unet
jwschroeder3
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Commits on May 2, 2019

Added support for false joins of distinct cells into single regions
jwschroeder3
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Merge pull request #121 from jwschroeder3/unet
jwschroeder3
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Commits on May 7, 2019

Track GUI for training data curation.
jwschroeder3
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Track GUI for training data curation.
jwschroeder3
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Merge pull request #122 from jwschroeder3/unet
jwschroeder3
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track gui
jwschroeder3
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Merge pull request #123 from jwschroeder3/unet
jwschroeder3
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Commits on May 9, 2019

note in track_gui
jwschroeder3
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Commits on May 13, 2019

Added segmentation model with dropout and normalization.
jwschroeder3
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Commits on May 14, 2019

Merge pull request #124 from jwschroeder3/unet
jwschroeder3
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Commits on May 15, 2019

Allow migration line to be drawn over multiple frames at once.
jwschroeder3
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Bug fix in migration line spanning multiple timepoints.
jwschroeder3
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More tracking GUI updates
jwschroeder3
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Commits on Jun 21, 2019

more updates to tracking gui
jwschroeder3
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Commits on Aug 7, 2019

plotting changes
jtsauls
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Commits on Aug 13, 2019

tracking algorithm and focus detection
jwschroeder3
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Commits on Aug 27, 2019

lots of changes since last push
jwschroeder3
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mm3.find_all_cell_intensities
jwschroeder3
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Commits on Aug 30, 2019

segmentation markup GUI sizing issues
jtsauls
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Commits on Sep 3, 2019

support for trimming big images before unet segmentation
jtsauls
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updated focus analysis
jwschroeder3
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Commits on Sep 5, 2019

filtering functions
jtsauls
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Commits on Sep 6, 2019

Commits on Sep 9, 2019

Updates to focus tracking and reporting
jwschroeder3
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updates to focus analysis
jwschroeder3
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Commits on Sep 10, 2019

__len__ method for Focus class
jwschroeder3
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Merge branch 'unet' of https://github.com/jwschroeder3/mm3 into unet
jwschroeder3
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__len__ method for Focus class
jwschroeder3
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Merge branch 'unet' of https://github.com/jwschroeder3/mm3
jwschroeder3
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cleaning up
jwschroeder3
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Commits on Sep 12, 2019

Commits on Sep 13, 2019

minor update to tracking model dictionary
jwschroeder3
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resolved conflicts
jwschroeder3
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Merge pull request #130 from jwschroeder3/master
jwschroeder3
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Commits on Oct 3, 2019

Started working on GUI for focus tracking
jwschroeder3
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Merge pull request #132 from jwschroeder3/master
jwschroeder3
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Commits on Oct 31, 2019

mm3_ChannelPicker.py
jwschroeder3
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Merge pull request #135 from jwschroeder3/master
jwschroeder3
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Commits on Nov 5, 2019

fixed segment-unet bug
jwschroeder3
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Merge pull request #136 from jwschroeder3/master
jwschroeder3
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generalized get_img parameter in mm3_curateTrainingData.py
jwschroeder3
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Merge pull request #137 from jwschroeder3/master
jwschroeder3
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Commits on Nov 6, 2019

bug fix in CellTrackGUI
jwschroeder3
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Merge pull request #138 from jwschroeder3/master
jwschroeder3
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Commits on Jan 9, 2020

New tracking models
jwschroeder3
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New tracking models
jwschroeder3
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Commits on Jan 17, 2020

added functionality for chtc
jwschroeder3
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added functionality for chtc
jwschroeder3
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some updates for chtc
jwschroeder3
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some updates for chtc
jwschroeder3
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Commits on Jan 21, 2020

more chtc updates
jwschroeder3
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more chtc updates
jwschroeder3
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Commits on Jan 23, 2020

updates to GUI
jwschroeder3
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updates to GUI
jwschroeder3
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Commits on Feb 19, 2020

allowing rotation of traps
jwschroeder3
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allowing rotation of traps
jwschroeder3
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Commits on Feb 20, 2020

Commits on Mar 3, 2020

trip
jwschroeder3
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trip
jwschroeder3
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Commits on Jul 30, 2020

cell-centric focus tracking
jwschroeder3
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cell-centric focus tracking
jwschroeder3
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Commits on Sep 4, 2020

focus track
jwschroeder3
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focus track
jwschroeder3
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Commits on Oct 30, 2020

switched to model.predict
jwschroeder3
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switched to model.predict
jwschroeder3
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switched to model.predict
jwschroeder3
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switched to model.predict
jwschroeder3
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Merge branch 'master' of https://github.com/jwschroeder3/mm3
jwschroeder3
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Merge branch 'master' of https://github.com/jwschroeder3/mm3
jwschroeder3
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fixing focus tracking
jwschroeder3
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fixing focus tracking
jwschroeder3
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fixing focus tracking
jwschroeder3
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fixing focus tracking
jwschroeder3
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Commits on Oct 31, 2020

fixed focus tracking
jwschroeder3
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fixed focus tracking
jwschroeder3
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Merge pull request #1 from jwschroeder3/focus_track
jwschroeder3
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Merge pull request #1 from jwschroeder3/focus_track
jwschroeder3
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Commits on Nov 4, 2020

switching focus tracking to deep learning
jwschroeder3
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switching focus tracking to deep learning
jwschroeder3
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Commits on Nov 6, 2020

deep learning workable
jwschroeder3
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deep learning workable
jwschroeder3
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Commits on Nov 9, 2020

deep learning workable
jwschroeder3
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deep learning workable
jwschroeder3
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deep learning workable
jwschroeder3
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Commits on Jan 8, 2021

updating for Fukang and Leah
jwschroeder3
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Commits on Jan 14, 2021

renamed aux folder to sup
jwschroeder3
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removed aux directory
jwschroeder3
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What is commit message?
fukangshe
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And this path needs to be changed as well
fukangshe
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Commits on Jan 15, 2021

Merge pull request #2 from fukangshe/dl_focus_track
jwschroeder3
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