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changelog.txt
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StitchIt Change-Log
20/09/2024
- Minor bugfixes
- Auto brain find is now disabled in sample splitter because it does not work with autoROI data.
21/05/2024
- Disable the auto brain finding button in the sample splitter. This is because under
some circumstances it draws ROIs that are too big and users are likely to accept this,
causing larger datasets for no reason.
18/04/2024
- BUGFIX: The INI file with missing fields was not being corrected and instead an empty file
that caused bugs was being made. This problem is now fixed.
02/12/2023:
- BUGFIX: Offset files are deleted when grand average is re-built. Failing to do this means
the two things are out of sync.
29/11/2023:
- BUGIFX: peekSection now honours the illumination correction setting.
- USER (Major): revert previous change to the offset subtraction, as it broke behavior in other systems (CS).
We need a better solution for OG.
22/06/2023:
- USER (Major): add new options for calculating background tiles. Valid options are now:
'offsetDimmestGMM' ('offsetDimest')
'averageTileMin' ('averageMin')
'averageTileMean'
'scanimage'
- USER (Major): Changes the way the offset of the average template is calculated. Now uses
the minimum of the average template. See: https://github.com/SainsburyWellcomeCentre/StitchIt/commit/19bfe8ea624840ff35a202286d69b5d5d6fd984c
This gets rid of horrible tiling artifacts that were plaguing a system and has had no obvious negative affect for some weeks under heavy testing.
- Minor bug fixes.
13/12/2021:
- USER Bugfix (Dev): updatechecker handles cases where stitchit is installed in a path that contains spaces. Add error report to git fetch step.
30/06/2021:
- USER:
Modify compression code so that cropped and stitched data can independently be set for compression.
The new INI file settings are:
;; The following two settings relate to whether the TIFFs should be compressed. Likely the
;; most sensible configuration if you want compression is to save compressed cropped images
;; but not compressed the stitched data, as these will discarded and compression slows down
;; processing.
;; save LZW compressed tiffs after stitching? Set to 0 for no compression and 1 for compression
saveCompressedStitched=0
;; save LZW compressed tiffs after cropping? Set to 0 for no compression and 1 for compression
saveCompressedCropped=0
Copy the above into your INI file.
21/06/2021:
- USER: add new stitching.saveCompressed feature to INI file. If this is set to 1 then TIFFs are saved LZW compressed. If it is set to 0, TIFFs are not compressed. By default TIFFs are not compressed (the current situation). After pulling this commit, you will receive a message stating:
Missing field saveCompressed in INI file /path/to/file/stitchitConf_local.ini. Using default value.
When the INI file is loaded.
You can get rid of the message by copying "saveCompressed=0" into the "[stitching]" section of the INI file.
Obviously set that to 1 if you want compression. For an example of what it should look like see the stitchitConf_DEFAULT.ini file.
04/06/2021:
- Bugfix : remove ":" characters from downsampled stack names
Also: have been working on code for fixing bidi scan errors. Code is in dev but sort of works and not documented. Merge to master anyway.
06/04/2021:
- Bugfix that was causing chessboard stitching to fail
30/03/2021:
- Bugfix to code that estimates sample end time.
25/03/2021:
- Ensure that all tile rows and columns are laid down. Bugfix.
11/02/2021:
- USER: downsampled stacks made at conclusion of acquisition for sampleSplitter
06/01/2021:
- USER - MAJOR: fixes bug that was losing the upper half of the dynamic range in stitched images.
- USER - stitchSection now handles an optional bidirectional phase correction. This is a fixed, user-provided,
value that must be an integer. e.g. stitchSection([100,1],2,'bidishiftpixels',-1)
14/11/2020:
- USER (made in dev branch): Update auto-thresh alg for web preview
- USER (made in dev branch): Provide helpful messages in sampleSplitter if stitched planes or downsampled stacks are missing
- USER (made in dev branch): Fix a couple of bugs that could cause stitching to fail.
12/11/2020:
- USER/DEVELOPER: sample splitter reports autoROI performance to stitchit log file [prerelease]
5/11/2020:
- Bugfix - Sample spliter was not reading the pixel size from the downsampled file names.
25/09/2020:
- Bugfix - since May 12th the sample splitter was not renaming acquisitions. Only directories. This is now fixed.
24/06/2020:
- User/DEVELOPER [branch dev]: downsampleAllChannels loads data only once for each resolution level.
09/06/2020:
- User/DEVELOPER [branch dev]: Remove TissueCyte settings from INI file. The TissueCyte settings are now gone from the StitchIt ini files. You should remove the [experiment], [micsPerPixel], and "Objectives" sections. See the stitchitConf_DEFAULT.ini file for an example.
13/03/2020
- DEVELOPER MAJOR: Dev branch. Drop TissueCyte support. StitchIt handles only BakingTray data now. There is a release associated with this commit. Refactor BakingTray stitching files and remove possibility of adding other stitching system systems. The flexibility isn't being used and it's worth the confusion.
- USER MAJOR: Stitching using stage positions now works.
11/06/2020
- USER: downsampled stacks now have illumination changes across depths corrected to a large degree
20/03/2020
- USER: Downsampled stacks now contain the channel name (as a string -- "red" or "green") in the file name.
- USER: stitchedPlanesToVolume produces stacks that contain the channel name the file name.
21/02/20
- MAJOR USER: New folder structure for downsampled stacks. *MAY BREAK BEHAVIOR OF DOWNSTREAM CODE*
23/01/2020
- USER: Sample splitter tidies away meta-data in sample root directory when finished.
07/10/19
- USER: Add "chessboardStitch.m" and "exploreChessboard.m" for assisting with stitching parameter tweaking.
03/10/2019
- USER: syncAndCrunch now *requires* the name of the acquisition system as an input argument
so we can handle multiple microscopes at once from one analysis PC.
26/09/2019
- USER: Slightly improve appearance of montage images in web preview.
05/06/2019
- USER: downsampleAllChannels makes TIFF files by default since
Elastix is now happy with these.
28/04/2019
- USER: The auto-threshold algorithm is tweaked to deal with small brain areas.
**Involves a small change in the threshold parameter** You will need to use
larger values and the cut-off before absolyte thresholding is now 25 not 10.
20/03/2019
- USER: Main web preview image is RGB.
- USER: New adaptive option for setting web preview threshold (see default INI file)
SUGGESTED ACTION: users modify their INI file such the rescale thresh=4 and the new comment text is
added in from the default INI file.
- USER: stitchit.sampleSplitter ready for beta use by users
15/03/2019
- USER: Add GUI (stitchit.sampleSplitter) for breaking up acquisitions with two brains into two separate
folders. Also allows cropping of a
single brain. GUI not heavily tested yet but it works.
02/01/2019
- Tidy files to make discovery of StitchIt features easier for users.
- DEVELOPER: New function "findStitchedData" to aid more flexible handling of already stitched data.
04/01/2019
- MAJOR: syncAndCrunch runs the web preview as a background task so it keeps up better with high bandwidth acquisitions.
You can now change which channel is being sent to the web by editing the file at /tmp/buildSectionRunnerTargetChannel so you you could do: echo "3" > /tmp/buildSectionRunnerTargetChannel
- mhd_write and the YAML reader are integrated into the repo, making instalation easier.
04/08/2018
- Bugfix: was failing to read z voxel size correctly.
- Now reads the most recent BakingTray recipe file, even if there are multiple.
13/07/2018
- MAJOR: syncAndCrunch has new call system! See "help syncAndCrunch" and note you need to edit your INI file. See the default INI file and https://github.com/BaselLaserMouse/StitchIt/wiki/Setting-up-syncAndCrunch
18/06/2018
- MAJOR - BakingTray tiles can be manipulated (undistorted and affine transformed) to allow for better stitching. User must edit StitchingParameters.VoxelSize in recipe to tweak mics per pixel if needed.
- MAJOR - Bugfix in BakingTray tile loader means the tileRotate parameter in the INI file will likely
need changing.
2018/05/02
- MAJOR: Allow for optional tile rotation during image loading. Note the new tileRotate argument to the INI file under the "tile" section.
- Average image tile collation is now only performed during syncAndCrunch for the first few sections and then again at the end.
2017/12/10
- preProcessTiles now takes paramater/value pairs as input arguments
- Image offset is read from ScanImage file header and is not calculated.
2017/10/16
- MAJOR: stitching-related parameters (including average images) are now stored in a separate location
to the raw data. So data sets processed prior to this date will need preprocessing again.
Suggest you first delete existing average images, as they take up a lot of space.
- Bugfix to cope with a situation where the user starts acquiring data from an extra channel mid-way
through the acquisition.
2017/10/10
- MAJOR: coefficients needed to stitch images (with the exception of the tileIndex) are now kept
in rawData/stitchitPreProcessingFiles/. You will need to update your INI file by copying
the relevant bit from the default INI file.
2017/10/06
- MAJOR: Offset subtraction is now set via the INI file. You will see warnings on screen until you add
this setting to your INI file.
- Improvements in the way the offset correction is performed.
- Remove calcAverageBinFiles since we now only calculate the newer .mat files
2017/09/21
- MAJOR: Enable offset correction in bakingtray.tileLoad. This seems necessary for Femto amps as they drift.
2017/09/21
- Bugfix to illumination corrector: error was generated if average file could not be found.
2017/07/13
- Average tiles saved as a structure.
- syncAndCrunch works with BakingTray where sections are saved directly to a "rawData" directory.
- Remove "averageSlowRows" option from INI file.
- Ability to stitch and average rectangular frames from BakingTray.
2017/05/11
- Improve docs and bug fix in stitchAllChannels.
2017/05/04:
- MAJOR: take away the option to remove channel 3 in syncAndCrunch
- BakingTray: moved to ScanImage multi-channels TIFFs. No longer reads split channels.
- Fix regression that was causing average image correction to fail with BT data
- Peeksection now stitches the first available channel by default. Not channel 2.
- DEVELOPER NOTE: meta-data format is now documented (help readMetaData2Stitchit)
- DEVELOPER NOTE: image processing moved out of tileLoad functions
2017/05/02
- Add makeCompositeOfPlane.m, which creates composite RGB images for use in Fiji with Bioformats
2017/03/12
- MAJOR: stitchAllSubDirectories is now stitchAllChannels. please see "help stitchAllChannels"
- MAJOR: The syncAndCrunch has new default values for the inputs:
* "combCorChans" argument now defaults to 1.
* "illumChans" argument now automatically selects all available channels.
* "chanToPlot" argument now automatically selects the first channel in illumChans.
- buildSectionPreview by default chooses the first available channel if none are provided.
- stitchSection will not proceed if the requested operation will fill the disk.
- syncAndCrunch does not proceed if local and server dirs are the same.
- Disk space reporter now works on Windows as well as Mac/Linux.
- Delete web directory (forWWW) at completion of syncAndCrunch.
- DEVELOPER NOTE: Minor bugfixes, cleanup (isfield calls relating to the INI file), mass tabs to spaces conversion.
2017/03/09
- MAJOR: identifyMissingTilesInDir now optionally replaces missing tiles with adjacent ones in the same x/y positition instead of blank tiles. (Merged commit from Natalia Chicherova, Fouga fork).
- Renamed postAcqfFun to postAcqFun in the INI file. (BREAKS EXISTING INI FILES)
2017/03/03
- saveMatrixAsCSV now runs on Windows.
- DEVELOPER NOTE: Read BakingTray v0.5 recipe files.
2017/02/28
- mergeChannels incorporates in place the addition, subtraction, etc, functions from Yunyun Han.
2017/02/21
- Seamless stitching bugfix so it works on more recent MATLAB versions.
2017/01/29
- syncAndCrunch checks if the user's repo is up to date (Unix only)
2017/10/19
- Fix bug that was causing stitching not to begin when acquisition ended.
- DEVELOPER NOTE: some syncAndCrunch errors are now being saved to a file called StitchIt_Log.txt in the sample directory. Aids debugging.
2016/11/22
- Go back to stitching *sections* in parallel instead of loading tiles in parallel. This is much faster.
2016/11/01
- DEVELOPER NOTE: BakingTray largely working. (beta feature)
2016/05/01
- Move repo to GitHub