Code

CNMF notebook update#1075

Code

Merged

EricThomson merged 65 commits intoflatironinstitute:devflatironinstitute/CaImAn:devfrom EricThomson:cnmf_notebook_updateEricThomson/CaImAn:cnmf_notebook_updateCopy head branch name to clipboardJan 25, 2024

+1,250-202

Commits

Commits on May 17, 2023

• starting work updating cnmf demo

  EricThomson

  committed
  aa98b56

  Copy full SHA for aa98b56

• updated intro section

  EricThomson

  committed
  e7fbc74

  Copy full SHA for e7fbc74

• updated logging section

  EricThomson

  committed
  f35aed2

  Copy full SHA for f35aed2

• updated logger explanation

  EricThomson

  committed
  b886161

  Copy full SHA for b886161

• updated file selection section

  EricThomson

  committed
  76d265e

  Copy full SHA for 76d265e

• added bit about multisession to file loading session

  EricThomson

  committed
  40e0030

  Copy full SHA for 40e0030

• path fixing

  EricThomson

  committed
  8ea1aec

  Copy full SHA for 8ea1aec

• movie viewer discussion added

  EricThomson

  committed
  0d1e821

  Copy full SHA for 0d1e821

• updated cluster setup section

  EricThomson

  committed
  6c73b34

  Copy full SHA for 6c73b34

• revised cluster setup description

  EricThomson

  committed
  4724dd5

  Copy full SHA for 4724dd5

• added temp placeholder image of workflow

  EricThomson

  committed
  e7f3d8b

  Copy full SHA for e7f3d8b

• added subindices discussion to movie player

  EricThomson

  committed
  5ef769d

  Copy full SHA for 5ef769d

• updated intro to parameter object

  EricThomson

  committed
  52309c9

  Copy full SHA for 52309c9

• edited parameter description

  EricThomson

  committed
  d7cb2f9

  Copy full SHA for d7cb2f9

• rebased to dev from master oops

  EricThomson

  committed
  a15d837

  Copy full SHA for a15d837

Commits on May 18, 2023

• updated handling of logging

  EricThomson

  committed
  82a1eda

  Copy full SHA for 82a1eda

Commits on Jun 5, 2023

• simplified download and added movie type info highlight

  EricThomson

  committed
  4a486d3

  Copy full SHA for 4a486d3

• simplified movie loading/viewing sections

  EricThomson

  committed
  a711340

  Copy full SHA for a711340

Commits on Jun 7, 2023

• updated through cluster

  EricThomson

  committed
  0b6351a

  Copy full SHA for 0b6351a

Commits on Jun 9, 2023

• motion correction section updated

  Show description for 098e3d4
  EricThomson

  committed
  098e3d4

  Copy full SHA for 098e3d4

Commits on Jun 10, 2023

• patch visualization wip

  EricThomson

  committed
  182633a

  Copy full SHA for 182633a

• cleared outputs

  EricThomson

  committed
  42ccedd

  Copy full SHA for 42ccedd

Commits on Jul 8, 2023

• updated notebook up through description of CNMF basic workflow

  EricThomson

  committed
  ffe18cd

  Copy full SHA for ffe18cd

Commits on Aug 3, 2023

• cnmf parameters explained and cnmf fit run

  EricThomson

  committed
  5bcdc1b

  Copy full SHA for 5bcdc1b

Commits on Aug 19, 2023

• fit and refit of cnmf model run

  EricThomson

  committed
  b85eea3

  Copy full SHA for b85eea3

Commits on Aug 21, 2023

• added discussion of estimates object

  EricThomson

  committed
  2bc6ce4

  Copy full SHA for 2bc6ce4

• component evaluation and estimate visualization

  EricThomson

  committed
  fe73cb7

  Copy full SHA for fe73cb7

Commits on Aug 22, 2023

• added custom visualization example

  EricThomson

  committed
  3ffa784

  Copy full SHA for 3ffa784

Commits on Aug 24, 2023

• show how to save and load results

  EricThomson

  committed
  fa73bfb

  Copy full SHA for fa73bfb

• missing docs added for load cnmf

  EricThomson

  committed
  bda449b

  Copy full SHA for bda449b

Commits on Aug 25, 2023

• dfof calculation and select components sections updated

  EricThomson

  committed
  e84ac78

  Copy full SHA for e84ac78

• play movie working

  EricThomson

  committed
  8b2f4bc

  Copy full SHA for 8b2f4bc

Commits on Aug 26, 2023

• final cleanup and movie visualizations added -- main notebook reno draft done!

  EricThomson

  committed
  5bf3e08

  Copy full SHA for 5bf3e08

Commits on Aug 27, 2023

• final changes in initial draft main notebook

  EricThomson

  committed
  0d0ce7e

  Copy full SHA for 0d0ce7e

Commits on Aug 29, 2023

• fixed problem with quilter

  EricThomson

  committed
  d26f513

  Copy full SHA for d26f513

Commits on Oct 9, 2023

• Merge branch 'dev' into cnmf_notebook_update

  EricThomson

  committed
  2ef412d

  Copy full SHA for 2ef412d

Commits on Oct 11, 2023

• updated draft through dff calculation

  EricThomson

  committed
  b44afa3

  Copy full SHA for b44afa3

• make sure detrend_df_f uses the use_residuals arg

  EricThomson

  committed
  aaff9d0

  Copy full SHA for aaff9d0

• update memory mapping discussion, add appendix

  EricThomson

  committed
  68e673d

  Copy full SHA for 68e673d

Commits on Oct 12, 2023

• updated memory mapping discussion

  EricThomson

  committed
  be0e0da

  Copy full SHA for be0e0da

Commits on Oct 15, 2023

• update rendering of max/corr images

  EricThomson

  committed
  c4e65a2

  Copy full SHA for c4e65a2

• updated discussion of important parameters and estimates class

  EricThomson

  committed
  7e40305

  Copy full SHA for 7e40305

• finished through main body of cnmf notebook

  EricThomson

  committed
  04317bd

  Copy full SHA for 04317bd

• cleaned up description of dfof

  EricThomson

  committed
  bb088b7

  Copy full SHA for bb088b7

• updated appendix on viewing large movies

  EricThomson

  committed
  e3aa562

  Copy full SHA for e3aa562

• added discussion of fastplotlib to Appendix 3

  EricThomson

  committed
  3f28b31

  Copy full SHA for 3f28b31

Commits on Oct 17, 2023

• added changes based on review suggestions

  EricThomson

  committed
  2ff8229

  Copy full SHA for 2ff8229

Commits on Oct 22, 2023

• removing appendices -- moved logging to Getting_Started.rst

  EricThomson

  committed
  55602a8

  Copy full SHA for 55602a8

• moved api discussion to docs

  EricThomson

  committed
  45260a1

  Copy full SHA for 45260a1

• cut cluster setup appendix, moved to docs

  EricThomson

  committed
  e9e2c32

  Copy full SHA for e9e2c32

• cut memmapping appendix, moved to docs

  EricThomson

  committed
  d1fba38

  Copy full SHA for d1fba38

• appendices all moved to sidebars and deleted

  EricThomson

  committed
  a9c1b4b

  Copy full SHA for a9c1b4b

Commits on Oct 24, 2023

• updated based on review, appendices to docs, etc

  EricThomson

  committed
  4e46230

  Copy full SHA for 4e46230

• Merge branch 'dev' into cnmf_notebook_update

  EricThomson

  authored
  ab91335

  Copy full SHA for ab91335

Commits on Oct 26, 2023

• minor typos and word-choice changes

  EricThomson

  committed
  f07c7f9

  Copy full SHA for f07c7f9

Commits on Dec 15, 2023

• removing excess verbiage

  EricThomson

  committed
  93cc1f6

  Copy full SHA for 93cc1f6

• cut and simplified notebook

  EricThomson

  committed
  cc4b31b

  Copy full SHA for cc4b31b

Commits on Jan 18, 2024

• preliminary save traces to csv added

  EricThomson

  committed
  5a7e15b

  Copy full SHA for 5a7e15b

Commits on Jan 19, 2024

• explain how to save results as csv

  EricThomson

  committed
  5fb4ab7

  Copy full SHA for 5fb4ab7

• Merge branch 'dev' into cnmf_notebook_update

  EricThomson

  authored
  30c9db2

  Copy full SHA for 30c9db2

• added explanation of dfof

  EricThomson

  committed
  70835d7

  Copy full SHA for 70835d7

Commits on Jan 22, 2024

• updated discussion of dff

  EricThomson

  committed
  6a1a813

  Copy full SHA for 6a1a813

• Merge branch 'cnmf_notebook_update' of https://github.com/EricThomson/CaImAn into cnmf_notebook_update

  EricThomson

  committed
  e2756eb

  Copy full SHA for e2756eb

• added caveat about time stamps

  EricThomson

  committed
  161e516

  Copy full SHA for 161e516

• gsig/gsiz just define what they are

  EricThomson

  committed
  fbf1418

  Copy full SHA for fbf1418