Programs for converting+combining/extracting tif to ims and the other way round, repairing erroneous pixel sizes and extracting a slice from a z-stack.

tif2ims: Receive a set of tif files that represent channels and combine them into a single file using the imaris format. The order of the channels in the output file is determined by the lexicographical order of the file names. Result is written to an ims file with the same file name prefix as the original.

For example, the output file created from the following files will have the channel order:

1. SLIDE-1895_4.0.4_R001_Cy3_CD86_FINAL_AFR_F.tif
2. SLIDE-1895_4.0.4_R001_Cy5_Pax5_FINAL_AFR_F.tif
3. SLIDE-1895_4.0.4_R001_Cy7_ERTR-7_FINAL_AFR_F.tif
4. SLIDE-1895_4.0.4_R001_DAPI__FINAL_F.tif

If we want to change the order we can modify the file name, after the common prefix, for instance:

1. SLIDE-1895_4.0.4_R001_01_DAPI__FINAL_F.tif
2. SLIDE-1895_4.0.4_R001_02_Cy5_Pax5_FINAL_AFR_F.tif
3. SLIDE-1895_4.0.4_R001_03_Cy7_ERTR-7_FINAL_AFR_F.tif
4. SLIDE-1895_4.0.4_R001_04_Cy3_CD86_FINAL_AFR_F.tif

ims2tif: Receive a set of ims files and extract the specified channel, time point and level in the image pyramid from each of the files. Result is written to tif file with the channel number, pyramid level and time point prefixed to the original file name.

For example, the output created for the file Barcode_1034_CollIV.ims when extracting channel 1, pyramid level 3 and timepoint 2 is c1_l3_t2_Barcode_1034_CollIV.tif. Note that all indexes (channel, pyramid level and timepoint are zero based).

repair_ims_size: Receive a csv file with four columns (file_name,x_in_um,y_in_um,z_in_um). The column file_name contains the paths to the files relative to the location of the csv file. The pixel sizes are in micrometers. Use this tool to repair/correct pixel sizes if they were incorrectly imported into imaris.

extract_slice: Receive a set of ims files and extract the specified slice (using percentage in z-stack, 0 - first slice, 0.5 - middle, 1.0 - last slice), and time point from each of the files. Result is written to ims file with the extracted slice number and time point postfixed to the original file name.

For example, the output created for the file Barcode_1034_CollIV.ims when extracting slice 2 and timepoint 0 is Barcode_1034_CollIV_s2_t0.ims. Note that all indexes (slice and time point are zero based).

1. Install miniconda if not already installed (download).
2. Download this repository (zip file).
3. Open the Anaconda Prompt (found under the Anaconda3 start menu).
4. Type the commands in the terminal window (don't forget to change the path_to_this_directory):

   cd path_to_this_directory
   conda env create -f windows.yml
   

5. Download the libvips zip file.
6. Copy it to this directory and unzip it.
7. Edit the run_tif2ims.bat, run_ims2tif.bat and run_repair_ims_size.bat files. Set the path to anaconda and path to vips library (see current batch file for example).

1. Double click the relevant file: run_tif2ims.bat, run_ims2tif.bat, run_repair_ims_size.bat, run_extract_slice.bat.

On OSX/Linux installation is easier, no need to download the libvips and set the path to it. Install conda env create -f osx_linux.yml and then edit the run_tif2ims.sh run_ims2tif.sh, run_repair_ims_size.sh files, updating the path to anaconda.

If run without any arguments, will open a GUI:

pythonw tif2ims.py

Notice that we use pythonw which is compatible with wxPython.

To run without a GUI provide the data directory and channel file name prefix on the commanadline, for example:

pythonw tif2ims.py data SLIDE-1895_1.0.4_R000