-
Notifications
You must be signed in to change notification settings - Fork 9
/
NEWS
200 lines (134 loc) · 5.46 KB
/
NEWS
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
Changes in version 0.1.0 (2020-01-16):
+ Initial commit
+ Creation of the SingleCellMapper package
+ Created inst/extdata folder with example images and data
+ Build the ImageList class
+ Created first unit tests for ImageList constructor
+ test
Changes in version 0.1.1 (2020-02-02):
+ Simplified structure of loadImages function
+ Created validity checks for path and file inputs
+ Fixed bugs to pass R CMD check
+ test
Changes in version 0.1.2 (2020-02-03):
+ channelNames generic function for Image and ImageList object
+ Reduced the size of example data
+ Wrote docs on data
Changes in version 0.1.3 (2020-02-16):
+ Full docs and tests on:
- ImageList-naming
- ImageList-subsetting
Changes in version 0.1.4 (2020-02-16):
+ Full docs and test on:
- loadImages
- ImageList-class
Changes in version 0.1.5 (2020-03-03):
+ plotCells function
+ plotPixels function
+ Options for further customization of scale_bar
+ Options for image_title customization
+ Started vignette draft
Changes in version 0.1.6 (2020-03-10):
+ Unit tests on plotCells and plotPixels
+ Improved setting colours
+ Rewrite to reduce validity checks
Changes in version 0.1.7 (2020-03-17):
+ Added scaleImages and normalize functions
+ Expanded shared parameters for plotPixels and plotCells
Changes in version 0.1.8 (2020-03-18):
+ Option to remove legend
+ Cleaned up representation of legend on plot
Changes in version 0.1.9 (2020-03-20):
+ scale, return_plot, return_images, legend, margin, display parameters
+ Finalised unit tests
Changes in version 0.1.10 (2020-03-21):
+ interpolate parameter
+ Bug fix to achieve correct aspect ratios
Changes in version 0.1.11 (2020-03-24):
+ Complete documentation of all package functions
Changes in version 0.1.12 (2020-03-25):
+ Renamed package from SingleCellMapper to cytomapper
+ Renamed ImageList class to CytoImageList class
Changes in version 0.1.13 (2020-03-28):
+ Full vignette and correction to docs
Changes in version 0.99.0 (2020-03-30):
+ Formatted the package for Bioconductor submission
Changes in version 0.99.4 (2020-04-01):
+ Fixed docs to pass checks on Windows
Changes in version 0.99.4 (2020-04-01):
+ Aesthetic changes to scale bar, image title and legend title
+ Removed channelNames as Image generic
+ removed exported plot method
Changes in version 0.99.5 (2020-04-10):
+ Added script to generate the toy dataset
+ Modified the toy dataset
+ Added more explanation on datasets to vignette
+ Bug fixes when colouring cells
+ Unit tests on all hidden functions
+ Account for over-saturation when merging colours
Changes in version 0.99.5 (2020-04-17):
+ Fixed labelling of colour legends
+ Corrected typos in docs and vignette
+ Avoid recalculation of min/max values in legend function
Changes in version 1.1.1 (2020-07-3):
+ Images are no longer re-normalized after channel merging (> 3 channels)
+ Instead images are clipped at 1 leading to brighter colours
+ The same happens for colour merging when colouring masks by feature expression
Changes in version 1.1.2 (2020-07-17):
+ Added shiny app to package
Changes in version 1.1.3 (2020-09-12):
+ Extended vignette
+ Changed package title
Changes in version 1.1.4 (2020-09-13):
+ Allow channel-specific inputRange inputs for normalisation
Changes in version 1.1.5 (2020-10-11):
+ Prepared for Bioc 3.12 release
+ Started unit testing the shiny app
Changes in version 1.1.6 (2020-10-23):
+ Dropped 32-bit Windows support
Changes in version 1.3.1 (2020-12-01):
+ Allow thick border contours
Changes in version 1.3.2 (2021-01-12):
+ Updated citation
Changes in version 1.3.3 (2021-01-24):
+ Added snapshot tests for shiny
+ Support win32 again
Changes in version 1.3.4 (2021-03-20):
+ Support on disk representation of images
Changes in version 1.3.5 (2021-04-07):
+ Added measureObjects function
Changes in version 1.3.6 (2021-04-23):
+ scaleImages accepts numeric vector value
Changes in version 1.5.1 (2021-05-19):
+ Bugfix: erroneous dimension setting when legend=NULL
Changes in version 1.5.2 (2021-09-15):
+ Added description on how to handle images with couplet/patchwork
Changes in version 1.5.3 (2021-09-16):
+ Added option to read in .h5 files
Changes in version 1.5.4 (2021-09-17):
+ It is not required anymore to specify exactly the right colours
Changes in version 1.7.1 (2021-12-28):
+ Added compImage function for channel spillover compensation
Changes in version 1.7.2 (2022-04-20):
+ Fixes for next release
Changes in version 1.9.1 (2022-07-24):
+ measureObjects function transfers mcols of images and masks to colData(sce)
+ allow returned object to be of SpatialExperiment
Changes in version 1.9.2 (2022-10-24):
+ measureObjects accounts for single objects in images
Changes in version 1.11.1 (2023-01-18):
+ Bug fix: set default dodge.width = NULL for geom_quasirandom
Changes in version 1.11.2 (2023-02-02):
+ Bug fix: measureObjects internally sets the correct channel names
Changes in version 1.11.3 (2023-01-23):
+ loadImages: added option to read in single-channel images to multi-channel
Changes in version 1.13.1 (2023-09-26):
+ loadImages: fixed pattern argument to only test on the actual files and not the path.
Changes in version 1.15.1 (2023-12-10):
+ the unit tests for compImage have now been adjusted to account for correct spillover induction
Changes in version 1.15.2 (2023-12-13):
+ change of package maintenance to Lasse Meyer
Changes in version 1.15.3 (2024-03-13):
+ measureObject fixes for Bioc 3.19 release
Changes in version 1.15.4 (2024-03-21):
+ measureObject fix reversion and test - Bioc 3.19